Re: [ccp4bb] help with wwPDB validation warning

[Eleanor Dodson]

Hmm - no idea but perhapd=s interesting that 0.83 ~ 1.7/2
Eleanor

On Fri, 7 Jun 2024 at 15:13, Aline Dias da Purificação <
d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
>
> I am currently validating a structure for deposition in the wwPDB and
> encountered the following warning in the validation system:
>
> Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or
> SigIo in SF file).
>
> The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShell, so I
> didn't understand the warning.
>
> Has anyone experienced this before and could assist me?
>
> Thank you.
>
> 
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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

[Eleanor Dodson]

Well, REFMAC output a (mislabelled)  F SIGF which was detwinned so if you
deposited the REFMAC output I guess that is detwinned..
Do you have the original REFMAC input still?
Eleanor

On Thu, 6 Jun 2024 at 15:18, Ben Bax  wrote:

> Hi,
>   I am just re-refining an old twinned dataset - which I will
> redeposit (refinement is never finished).
> The pdb seem to have automagically detwinned my data.
> Where do I find my original twinned data (F and SIGF)? (or will I have
> to redeposit my original un-detwinned structure factors).
>  Thanks, Ben
>
>
>
> On Fri, May 31, 2024 at 4:36 PM Ezra Peisach
>  wrote:
> >
> > In fall of 2024, electron density map coefficients will be available in
> > the public PDB archive for all X-ray structures. These map coefficients
> > will be the same as used in wwPDB Validation Reports.
> >
> > The new map coefficients files will replace the electron density maps
> > and combined map coefficient files calculated and distributed by RCSB
> > PDB and used by the NGLviewer at RCSB.org. These data (served by
> > EDMAPS.rcsb.org) are calculated using publicly-available coordinate
> > files and structure factor files and offered in DSN6 formatted map files
> > and MTZ formatted map coefficient files. RCSB PDB plans to shutdown the
> > NGL viewer by July 2024
> > (https://www.rcsb.org/news/feature/65b42d3fc76ca3abcc925d15) and will no
> > longer need the data served by EDMAPS.rcsb.org.
> >
> > RCSB PDB will be phasing out EDMAPS.rcsb.org:
> >
> >   *  June 28, 2024: DSN6-formatted map files will no longer be
> > provided. EDMAPS.rcsb.org will only serve MTZ files with map
> coefficients.
> >   *  Fall 2024: Electron density map coefficients will be available
> > in the public PDB archive for all X-ray structures. At this point,
> > EDMAPS.rcsb.org will be shut down, including access to MTZ files with
> > map coefficients from this service.
> >
> > To help users with this transition, RCSB PDB will be holding a Virtual
> > Office Hour on Thursday June 13, 2024 from 1:00pm-2:00pm Eastern,
> > 10:00am-11am Pacific. Please register online for this event at
> > https://go.rutgers.edu/psx4pr63.
> >
> > Questions about this transition or the Virtual Office Hour can be sent
> > to i...@rcsb.org.
> >
> > 
> >
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Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

[Eleanor Dodson]

Hmm - rather tricky! I would do an MR search with the crystal model v the
EM density,
Steps would be:
1) convert EM density to "structure factors". - there are tools which do
this ..
  1a) You need to go back to ccp4i - program sfall to read map to generate
SFs from map - then cad or sftools to add a fake SigF column
2) Solve MR search with the model v these "structure factors" using them
as Fobs
3) Calculate the structure factors from the MR positiooned model and get
the difference map..


On Wed, 5 Jun 2024 at 11:46, Martin Malý  wrote:

> Dear Devbrat,
>
> I am now playing with a similar problem but I don't have a simple solution
> for you as I'm also quite stuck. You can check these software tools which
> involve some scripting in Python (NumPy, SciPy) and C++:
>
> EMDA (for cryoEM maps, included in CCP-EM)
> https://gitlab.com/ccpem/emda
> https://doi.org/10.1016/j.jsb.2021.107826
>
> Gemmi (mainly for crystallography, included in CCP4)
> https://gemmi.readthedocs.io/en/latest/grid.html
>
> Maybe there are also some relevant features in CCTBX (included in CCP4 and
> Phenix).
>
> Cheers,
> Martin
>
> On 05/06/2024 07:00, Devbrat Kumar wrote:
>
> Hello Everyone,
>
> Greetings!
>
> I have a query regarding the resampling of cryoEM density to match crystal
> density to obtain a density difference map. Specifically, I am trying to
> determine if it is feasible to resample a cryoEM map with an XRD density
> map. However, each time I attempt this, the resampling output provides an
> arbitrary ASU resample map, resulting in a significant loss of major
> density.
>
> I have been using Coot and Chimera for this process but have not achieved
> the desired outcome. Please guide me or suggest how to move forward with
> this. My goal is to create an accurate final density difference map.
>
> Thank you in advance for your help.
> *Warm Regards-*
> *Devbrat Kumar*
>
>
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Re: [ccp4bb] valine difference map interpretation

[Eleanor Dodson]

Your pictures 1 3 & 4 don't seem to show multiple occupancy? Maybe the
difference map 2 is saying - too much complexity ??
Eleanor

On Thu, 30 May 2024 at 23:29, Michael Colaneri 
wrote:

> Dear All,
> We have alternate conformations for a number of residues in a structure
> and one is a Val that I show in the attachment.  It was refined with group
> occupancy and the temp factors are fine.  It was also present in an early
> map from autobuild at a time it was not in the model.
>
> The question I have is why the difference map looks this way.  Is it
> inadequate temp factor/occupancy model, high thermal motion, bulk solvent
> in the region, disorder of some sort? I would appreciate any help.
>
> Thank you.
>
>
> --
>
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Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

[Eleanor Dodson]

With that translation (x,1/2,1/2) lots of your reflections with k and l
 Odd will be relatively weak and those zones usually have higher r factors.
Look at the plots of reflection zones in hklview and you will probably
notice weak and strong zones.

The translation will make selecting the soacegroup a bit tricky but if you
ran molrep and tested all spacegroups in the pointgroup Thst usually
clearly suggests the right one.

On Wed, 29 May 2024 at 15:05, Esko Oksanen <
533d495de740-dmarc-requ...@jiscmail.ac.uk> wrote:

>   Hi Cat,
>
>   If your pseudo-centering actually leads to significant change in your
> cumulative intensity distribution, you might have a convincing explanation
> as to why the R-values would remain on the high side. I had a pseudo-body
> centered case a long time ago (https://doi.org/10.1107/s0907444906031519)
> and there the R-values remained a lot higher.
>
>   HTH,
>   Esko
>
> On 29 May 2024, at 15:48, Catherine Back <
> d42dc456258a-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi,
>
> I have collected data for a protein which solved easily to 1.6 Å using MR.
> However, during data analysis and refinement it clearly has translational
> NCS. According to Xtriage on Phenix:
> Frac. coord.: 0.072, -0.498, 0.5
> Distance to origin: 68.798
> Height relative to origin: 51.479%
> p-value (height): 5.577e-05
>
> Wilson value and L-test suggests no twinning.
>
> It solved using Molrep in ccp4i2. P2 21 21. All stats look good, but even
> after refinement (not fully and completely finalised yet) R= 0.24 and
> Rfree=0.27. Also, it appears the 2 molecules in the AU have swapped a helix
> with their respective symmetry partners. I'm pretty sure I now have the
> correct space group, and tried various others with much less success.
>
>
>1. Will these Rfactors be 'good'/low enough to publish for a dataset
>at 1.6Å?
>2. Should I be doing anything else during structure solving to
>alleviate the effects of tNCS? (I did try using Phaser to solve the
>structure, but the stats were much worse and even though 'tNCS is present
>correction factors were not applied'. I'm not sure why.
>
>
> Many thanks,
> Cat
>
> Dr Catherine R. Back (she/her)
> Senior Post-doctoral Research Associate
> School of Biochemistry
> University of Bristol
> UK
>
>
>
>
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Re: [ccp4bb] Modeling Disulfide Bond Occupancies

[Eleanor Dodson]

But are there two conformations of the disulphide? or one disulphide and
one broken link?
Eleaor

On Mon, 6 May 2024 at 20:42, Dr. Kevin M Jude  wrote:

> I have done this in shelxl or phenix refinement, you can define occupancy
> groups (or free variables in shelxl) so that 472A and 384A are one group,
> 472B and 384B are another. Pretty sure there is a similar solution in
> refmac. Though also if the 384A rotamer doesn’t clash with the 472B
> rotamer, you could have three states A/A (disulfide), A/B (no disulfide),
> B/B (no disulfide).
>
>
>
> --
>
> Kevin Jude, PhD
>
> Structural Biology Research Specialist, Garcia Lab
>
> Howard Hughes Medical Institute
>
> Stanford University School of Medicine
>
> Beckman B177, 279 Campus Drive, Stanford CA 94305
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of Liliana
> Margent 
> *Date: *Monday, May 6, 2024 at 12:20 PM
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *[ccp4bb] Modeling Disulfide Bond Occupancies
>
> Greetings everyone,
>
> I'm currently in the process of modeling a disulfide bond in two
> structures. However, when I attempt to model single occupancy for the
> cysteines involved in the bond, negative density blobs emerge within the
> disulfide bond. This suggests the possibility of alternate conformations
> for the cysteines.
>
> Yet, when I endeavor to model alternate conformations for both cysteines,
> their occupancies do not align despite running refinement with a bond
> parameter file that specifies the link. To illustrate, I initiate the
> refinement with occupancies for Cys472 as A0.75/B0.25 and for C384 as
> A0.75/B0.25, but post-refinement, the output occupancies appear as Cys472
> A0.84/B0.16 and for C384 A0.97/B0.03. Where A confs participate in the s-s
> bond.
>
> Has anyone else encountered this issue before, or does anyone have
> suggestions on how to refine these cysteines to achieve coherent
> occupancies?
>
> Thank you for any insights you can provide.
>
> Best,
> Liliana
>
> 
>
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Re: [ccp4bb] Modeling Disulfide Bond Occupancies

[Eleanor Dodson]

Well - I turn off occupancy refinement once there is a sort of consensus..
Disulphides often break after long exposures and you see the positive and
negative blobs clearly. I must admit I usually just set 0.5 as occ , fix
the surviving disulphide link and let the B values suggest a better ratio
than o.5:0.5..
Eleanor

On Mon, 6 May 2024 at 20:20, Liliana Margent 
wrote:

> Greetings everyone,
>
> I'm currently in the process of modeling a disulfide bond in two
> structures. However, when I attempt to model single occupancy for the
> cysteines involved in the bond, negative density blobs emerge within the
> disulfide bond. This suggests the possibility of alternate conformations
> for the cysteines.
>
> Yet, when I endeavor to model alternate conformations for both cysteines,
> their occupancies do not align despite running refinement with a bond
> parameter file that specifies the link. To illustrate, I initiate the
> refinement with occupancies for Cys472 as A0.75/B0.25 and for C384 as
> A0.75/B0.25, but post-refinement, the output occupancies appear as Cys472
> A0.84/B0.16 and for C384 A0.97/B0.03. Where A confs participate in the s-s
> bond.
>
> Has anyone else encountered this issue before, or does anyone have
> suggestions on how to refine these cysteines to achieve coherent
> occupancies?
>
> Thank you for any insights you can provide.
>
> Best,
> Liliana
>
> 
>
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Re: [ccp4bb] refmac5 version 5.8.0425 corrupts B-factors..?

[Eleanor Dodson]

That result looks really bizarre  but it is hard to make a sensible comment
without more details..maybe you could attach the whole log file for the
refmac run.

What input reflection dAta are you using ? You couldn’t have picked up a
Sharpened set by any chance? (It is always good practice to make sure you
are using the original merged set.)
Good luck Eleanor




On Sat, 27 Apr 2024 at 07:39, Kay Diederichs 
wrote:

> Dear Martin,
>
> one suspicion comes to my mind: could it be a "computer problem" in the
> sense that you are using different computing environments for the two
> calculations (arpWarp vs standalone refmac5)? That could lead to different
> decimal separators ("." versus a ","; see
> https://en.wikipedia.org/wiki/Decimal_separator ). This could happen for
> - different computers or operating systems
> - different users, because each user can set the LANG individually
> In my experience with this problem, it shows e.g. in coot by distorted
> bonds and the like. And I do see in your screenshot that the coordinates
> differ between your two runs.
> The workaround is to set the LANG to C:
> export LANG=C
> if you use the bash shell (similarly in other shells), before starting
> calculations.
>
> Anyway, you could report which computing environment you use, maybe that
> gives a hint.
>
> Hope this helps,
> Kay
>
> On Fri, 26 Apr 2024 17:59:07 +, Martin Moche 
> wrote:
>
> >Dear CCP4bb,
> >
> >I have a high resolution 1.4� dataset, and running arpWarp after MR and
> make almost all model building required.
> >
> >After arpWarp, my model and data fit excellent to each other, R-value
> around 20, and a few residues in the terminii remains to be fixed.
> >
> >When I send the output from arpWarp to refmac5, the B-factor column gets
> corrupted pictures in attached PDF, and R/Rfree increase to 0.26/0.28 and
> "Correlation Coefficient Fo-Fc" are also worsening.
> >
> >The arpWarp routine uses the same refmac5 version 5.8.0425 as "refmac5
> itself".
> >
> >I tried refmac5 in both CCP4 017 and 019, using the same refmac5 version
> 5.8.0425, and B-factor column gets corrupted in both.
> >
> >Best regards,
> >Martin
> >
> >P.S.
> >phenix.refine has no problems and R/Rfree remains at 0.20/0.22...
> >D.S.
> >
> >Head of Macromolecular X-ray Crystallography
> | Protein Science Facility
> >Medical Biochemistry and Biophysics<
> https://ki.se/en/mbb/department-of-medical-biochemistry-and-biophysics>
> >171 65 Solna | Solnav
> �gen
> 9
> >+46 8 524 868 43 | +46 73 322 93 27
> >martin.mo...@ki.se | ki.se
> >__
> >[cid:image001.png@01DA9812.F040E8F0] >[cid:image002.jpg@01DA9812.F040E8F0]
> [cid:image003.png@01DA9812.F040E8F0] 
> >
> >
> >
> >
> >
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Re: [ccp4bb] Rescale merged data?

[Eleanor Dodson]

If you are using CCP4I2 and use the task "Import merged data" that sort of
reprocesses that data through AIMLESS. You get all the usual graphsv
resolution - completeness, I/SigI , Wilson plot, Second moments etc and
from those can make a sensible decision on where the resolution limit
should be set..
In my experience rescaling isnt usually necessary - the scales are weighted
by SigI and very weak data has little effect..
Eleanor

On Thu, 18 Apr 2024 at 09:22, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi
>
> Only comment is that (surely) any decent refinement program these days
> would down-weight any reflections with negligible I/sig(I) (for example,
> those in the “unobserved” high resolution regions) so that they do not
> contribute (significantly) to the refinement. Or am I wrong (I don’t mind
> being wrong, and since I am a little rusty in these mattrers I would be
> very happy to be educated)?
>
> Doesn’t Aimless produce a table with the cumulative statistics at various
> resolution limits? So you don’t even need to re-scale & merge to get the
> stats to whatever your chosen high resolution limit is (I’d choose CC -1/2
> = 0.30, as Doeke suggests)? Do HKL or XSCALE do the same (sorry, I haven’t
> looked at their output for quite some time)?
>
> Just my two ha’porth
>
> Harry
>
> > On 17 Apr 2024, at 21:35, Hekstra, Doeke Romke <
> doeke_heks...@harvard.edu> wrote:
> >
> > Hi Matt,
> >
> > I appreciate disagreement and comments from colleagues. My two cents are
> that it seems unnecessary to repeat scaling and merging, or any earlier
> step. If you want to remove structure factor amplitudes or merged
> intensities from the MTZ file you can do so using MTZUTILS or similar
> functionality in CCP4 (
> https://www.ccp4.ac.uk/html/mtzutils.html#generalresolution). For
> refinement, you can specify the desired resolution range in your favorite
> refinement program.
> >
> > My personal convention is to use CC1/2 = 0.30 as the point to which
> retain data and  = 2 as the nominal resolution of the dataset. If
> you have the HKL2000 scaling log, you should be able to retrieve this
> information. I frankly wish we’d just deposit all data in the PDB rather
> than truncate based on some criterion or another.
> >
> > Best, Doeke
> >
> > From: Matt Mcleod 
> > Sent: Wednesday, April 17, 2024 4:12 PM
> > To: Hekstra, Doeke Romke 
> > Cc: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Rescale merged data?
> >
> > Sure thing.
> >
> > A former student left somewhere between 30-50 datasets but they scaled
> the data to the detector corners (or maybe edge) in HKL2000.  There are
> many of the high-resolution bins with no reflections in them.  He then went
> forward and merged this data, presumably in HKL2000 again and did his model
> building/refinement.   We now need to re-refine the models against this
> data for publication but we need a more suitable resolution cutoff for the
> data.
> >
> > Rather than go back and index/integrate all the data and then rescale
> the data to a more appropriate place (then merge), I was wondering if there
> was a way to take the merged reflections as either .sca or .mtz (from
> scalepacktomtz output) and then rescale to a more appropriate resolution.
> It doesn't seem like the student left unmerged data.
> >
> > So, nothing fancy (aniostropy etc), there is just a lot of data that
> needs to be adjusted and I am trying to avoid reprocessing all the frames
> again.
> >
> > Matt
> >
> > On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke <
> doeke_heks...@harvard.edu> wrote:
> > Hi Matt,
> >
> > It would be helpful if you could describe your case in more detail. Do
> you want to change the resolution cutoff after scaling? Do you want to keep
> more data? Fewer? Or do you mean something different such as truncation to
> generate amplitudes, application of anisotropic resolution cutoffs,  or
> outlier rejection? Are you referring to data that were scaled in HKL2000?
> >
> > Best, Doeke
> >
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Matt
> McLeod
> > Sent: Wednesday, April 17, 2024 3:04 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] Rescale merged data?
> >
> > Hi all,
> >
> > I am looking at a old students data and it looks like they didn't
> properly cut off the data during scaling.  All of the files I have appear
> to be the merged .sca (or mtz after converting with scalepacktomtz) - is
> there a way to retruncate the data after merging or do I have to reprocess
> the data?
> >
> > Thanks,
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
> >
> > --
> 

Re: [ccp4bb] How to compare the same protein crystallized in different conditions?

[Eleanor Dodson]

I like to use difference maps between Fa and Fb ..
It is a bit tricky now to set them up..but they do highlight changes.

Obviously
1) you need to have the same spacegroup and cell, and the same indexing
convention.
(Easy to check this in the data processing task when importing the second
data set. - give the first data set as a reference)

2) Dont be tempted to run molecular replacement on the second structure -
just start refinemen from structure 1) - it is MUCH simpler if both
examples are on the same origin..


Now maybe you go back to the old fashioned ccp4i.

Run CAD to put both sets (and associated phases for one of the structures)
into a single mtz
Run SCALEIT to a) put the two data sets on the same scale, and b) look for
a sensible resolution to choose, and to pinpoint any unlikely differences
that could dominate a difference map..
Then I run the old FFT task where you could input these cut offs easily,
but maybe it is possible with the newer program?? No documentation though
that I could find..
The FFT map can then be read into COOT (dont forget to mark it as a
difference map)
And a peak search will highlight large positive and negative regions
Positive where there is something in structure 1) but not in 2)
Negative where there is something in structure 2) but not in 1)

Easy-peasy??? well - it really is informative!
Eleanor



On Tue, 9 Apr 2024 at 08:33, Briony Yorke  wrote:

> Hi Murpholino,
>
>
>
> Helen Ginn is developing software to characterise changes in protein
> structures (especially informative when the changes are small but
> significant)– there is a web app and a download here:
>
>
>
> https://rope.hginn.co.uk
>
>
>
> I recommend watching the youtube tutorial.
>
>
>
> *From: *CCP4 bulletin board  on behalf of
> Murpholino Peligro 
> *Date: *Tuesday, 9 April 2024 at 02:39
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *[ccp4bb] How to compare the same protein crystallized in
> different conditions?
>
> *Caution External Email:* Do not click any links or open any attachments
> unless you trust the sender and know that the content is safe.
>
> Hi...
>
> Let's say I want to compare the same protein crystallized in different
> conditions. Same space group, almost same resolution. The global RMSD will
> be pretty small (around 0.3 Angstroms). There will be some changes in
> rotamers in some residues and some extra waters here and there... Besides
> local rsmd and contact maps (or differences in contact maps)... is there
> anything else to get a decent view of these small changes?
>
> Thanks a lot.
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] request for applications

[Eleanor Dodson]

It. Will probably take me  a. Full year to draft the. Application - is that
too slow?

On Mon, 1 Apr 2024 at 09:22, Frank Von Delft <
bcb385fe5582-dmarc-requ...@jiscmail.ac.uk> wrote:

> Oh dear, your prime number oversupply crashed the crypto Ponzi scheme
> market.  Will you accept $10e2 proposals now?
>
> Sent from tiny silly touch screen
> --
> *From:* James Holton 
> *Sent:* Monday, 1 April 2024 08:01
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] request for applications
>
> Hey Everyone,
>
> It may sound like an incredibly boring thing that there has never been a
> formal mathematical proof that finding the prime factors of very large
> numbers doesn't have a more efficient algorithm than simply trying every
> single one of them. Nevertheless, to this day, encryption keys and
> indeed blockchain-based cryptocurrencies hinge upon how computationally
> hard it is to find these large prime factors. And yet, no one has ever
> proven that there is not a more efficient way.
>
> It occurred to me recently that cryptocurrencies (blockchains) are
> nothing more than a sequence of numbers, and Large Language Models
> fundamentally take a sequence of "words" and predict the next one in the
> series. So, they seem naturally suited to the task of finding a more
> efficient way. I spent some of my free time trying my hand at this.
> There were some twists and turns along the way, but as of today it seems
> to be working. Predictions are now coming pretty fast. By the end of
> April 1, I expect to have ~ $1e12 USD on current ledgers. This may have
> certain socioeconomic ramifications, but that is not what I want to
> discuss here. What I want to discuss is how to use this new source of
> scientific funding!
>
> My question for the BB is: what would YOU do if you had $1e12 USD for
> your science? No non-scientific proposals please. There are plenty of
> other forums for those.  This BB is about biological structural science,
> so please stay on-topic.  OK?  And now: suggestions!
>
> I am particularly interested in projects that can only be done with a
> large, cooperative $1e12 USD, but not by 10e6 independent and unrelated
> $100e3 projects. The Apollo moon missions, for example cost $300e9
> (adjusted USD).  On a smaller scale, re-doing the whole PDB from cloning
> and expression to crystallization and structure solution would only cost
> about $500e6 USD. That would finally give us a good database of
> crystallization conditions for training an AI to tell you, given a
> sequence, what the crystallization conditions (if any) will be. That
> might take a lot of computing power, but there is plenty left over to
> buy 10 zettaflops of computing power (and the solar panels needed to
> power it). Or, if we really want to just divide it up, that would be
> $10e6 for each of the ~1e5 people on this planet who fit into the
> category of "biological scientist". That's not just PIs, but postdocs,
> grad students, techs. Everybody.
>
> I'm sure this will solve a lot of problems, but not all of them. And, I
> like to get ahead of things. So, what are the non-financial problems
> that will remain?  I think these are the most important problems in
> science: the intellectual and technological hurdles that money can't
> overcome.  I'm hoping this will be an opportunity for all of us to focus
> on those.  I know we're all not used to thinking on this scale, but, at
> least for today, let's give it a try!
>
> Looking forward to your applications,
>
> -James Holton
> MAD Scientist
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> --
> *From:* James Holton 
> *Sent:* Monday, 1 April 2024 08:01
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] request for applications
>
> Hey Everyone,
>
> It may sound like an incredibly boring thing that there has never been a
> formal mathematical proof that finding the prime factors of very large
> numbers doesn't have a more efficient algorithm than simply trying every
> single one of them. Nevertheless, to this day, encryption keys and
> indeed blockchain-based cryptocurrencies hinge upon how computationally
> hard it is to find these large prime factors. And yet, no one has ever
> proven that there is not a more efficient way.
>
> It occurred to me recently that cryptocurrencies (blockchains) are
> nothing more than a sequence of numbers, and Large Language Models
> fundamentally take a sequence of "words" and predict the next one in the
> series. So, they seem naturally suited to the task of finding a more
> efficient way. I spent some of my free time trying my hand at 

Re: [ccp4bb] mixture

[Eleanor Dodson]

This is best done by calculating  the structure factors for the part you
want to fix. (make sure the occupancies are set yo 0.8)
The REFMAC hklout will contain F SIGF etc plus FCALC PHIcalc for that bit
Define this file as your input hkl
Then refine the 20% structure (occs=0.2) with input
LABI FP=F SIGFP=SIGf  FPARTi=FCALC_80% PHIPARTi-PHIC
THis will refine the 20% part and add on the structure factors from the 80%
without any refinement of that..
Eleanor


On Tue, 5 Mar 2024 at 13:32, Martin Malý  wrote:

> Dear Marius,
>
> could the 'refinement exclude' keyword for refmac5 help?
> refinement exclude all from [residue] [chain] to [residue] [chain]
>
> Best regards,
> Martin
>
> On Tue, 2024-03-05 at 14:06 +0100, Ilme Schlichting wrote:
>
> Dear Marius,
>
> Thomas discussed this issue in great detail in the supplement of our
> recent publication
> https://www.nature.com/articles/s41586-024-07032-9
>
> Good luck,
>
> Ilme
>
> On 28/02/2024 17:43, Marius Schmidt wrote:
>
> Dear All,
> can someone quickly update me with a
> way to refine a mixture of structures in
> refmac or phenix.
> For example, the mixture consists of
> 80 % structure 1 and 20 % structure 2.
> It is important that structure 1 is kept
> fixed (is not refined) and only structure
> 2 is varied.
>
> Best
> Marius
>
>
> Marius Schmidt, Dr. rer. Nat. (habil.)
> Professor
> University of Wisconsin-Milwaukee
> Kenwood Interdisciplinary Research Complex
> Physics Department, Room 3087
> 3135 North Maryland Avenue
> Milwaukee, Wi 53211
> phone (office): 1-414-229-4338
> phone (lab): 414-229-3946
> email: smar...@uwm.edu
> https://uwm.edu/physics/people/schmidt-marius/
> 
> https://sites.uwm.edu/smarius/ 
> https://www.bioxfel.org/ 
> Nature News and Views:
> https://www.nature.com/articles/d41586-023-00504-4
> 
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] RES: [ccp4bb] Rwork and Rfree the same?

[Eleanor Dodson]

That is extremely likely! - certainly REFMAC will do that..
If 5% missing using DFcalc is a good thing - if 35% is missing not wise..
Eleanor

On Mon, 4 Mar 2024 at 07:53, Ben Bax  wrote:

>
> Fcalc maps look fantastic. Are you sure they were not using an Fcalc for
> the missing 35% of the data?
>   Ben
>
>
> On 29 Feb 2024, at 21:33, Rafael Marques 
> wrote:
>
> Sorry for jumping into the post, but I would like the community’s opinion
> about completeness, once this topic was raised here. What could be
> considered reasonable? Recently I have seen a 65% completeness Crystal
> structure and, surprisingly, the electron density map was not that bad for
> a > 3.2 A structure. How such a nice map could have been calculated with
> such poor parameters? I could only think of anisotropy.
>
> Best
>
>
> Rafael Marques da Silva
> PhD Student – Structural Biology
> University of Leicester
>
> Mestre em Física Biomolecular
> Universidade de São Paulo
>
> Bacharel em Ciências Biológicas
> Universidade Federal de São Carlos
>
> phone: +55 16 99766-0021
>
> *   "A sorte acompanha uma mente bem treinada"*
> **
>
> --
> *De:* CCP4 bulletin board  em nome de Paul Adams <
> pdad...@lbl.gov>
> *Enviado:* Wednesday, February 28, 2024 2:58:16 PM
> *Para:* CCP4BB@JISCMAIL.AC.UK 
> *Assunto:* Re: [ccp4bb] Rwork and Rfree the same?
>
>
> By setting wxc (weight of the X-ray term) to 0.1 there is good chance that
> the refinement is dominated by the geometry term and the model isn’t really
> seeing the effect of the X-ray data. I suspect this would result in
> R-factors that are similar. Why they are so low is less clear, but as
> others have pointed out 38% completeness is a problem. It would be good to
> check if that is 38% overall, or just very incomplete in the higher
> resolution shells. If it is complete at lower resolution you might be able
> to do something with the dataset, but not using the default
> parameterization in refinement programs - you’ll need to apply constraints
> and additional restraints if you can, and look at the weighting (by
> modifying wxc_scale, not wxc).
>
> There is a Phenix mailing list you might want to use as well (I assume you
> are using phenix.refine):
> https://phenix-online.org/mailman/listinfo/phenixbb
>
> On Feb 28, 2024, at 8:21 AM, Justin Cruite 
> wrote:
>
> Thanks everyone,
>
> I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å dataset.
> The data was processed using autoProc and the staranisano mtz was used for
> MR. The completeness is only 38%. It could be that the Rfree and Rwork
> reflection sets are small because of this? What is the best way to check
> the number of reflections used for Rwork and Rfree? Is this dataset usable
> at all?
>
> Thanks!
>
> Justin
>
> On Wed, Feb 28, 2024 at 10:21 AM nicfoos  wrote:
>
> Hello Justin,
>
> There is something weird in your results. You mention Rwork/Rfree of
> 0.1837.
> This means a pretty good refinement and also is very unusual to be
> obtain for a resolution of 3.37.
> Additionally you should not have Rfree = Rwork.
> I suspect something wrong with you Rfree reflections sets. What size is
> it ? Is your dataset complet ?
> How did you cut the res. ?
>
> I hope this may help you.
>
> Nicolas
>
>
>
> On 2024-02-28 16:10, Justin Cruite wrote:
> > Hi everyone,
> >
> > What does it mean if your Rwork and Rfree are exactly the same?
> >
> > I solved a 3.37 Å structure with Phaser-MR and immediately ran 10
> > cycles of refinement with wxc = 0.1. Everything else at default. The
> > Rwork and Rfree are both 0.1837. Is this bad?
> >
> > Thank you!
> >
> > Justin
> >
> > -
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
> Paul Adams (he/him/his)
> Associate Laboratory Director for Biosciences, LBL (
> https://biosciences.lbl.gov)
> Principal Investigator, Computational Crystallography Initiative, LBL (
> http://cci.lbl.gov)
> Vice President for Technology, the Joint BioEnergy Institute (
> http://www.jbei.org)
> Principal Investigator, ALS-ENABLE, Advanced Light Source (
> http://als-enable.lbl.gov)
> Laboratory Research Manager, ENIGMA Science Focus Area (
> http://enigma.lbl.gov)
> Adjunct Professor, Department of Bioengineering, UC Berkeley (
> http://bioeng.berkeley.edu)
> Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (
> http://compbiochem.berkeley.edu)
>
> Building 91, Room 410
> Building 978, Room 4126
> Tel: 1-510-486-4225
> http://cci.lbl.gov/paul
> ORCID: -0001-9333-8219
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 91R0183
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Michael Espinosa [ 

Re: [ccp4bb] Rwork and Rfree the same?

[Eleanor Dodson]

Well REFMAC tells you how many reflections are used..
And if you do
mtzdmp data.mtz

that will tell you too..
With such low completeness R factors are pretty meaningless - you must have
many more parameters than observations so that does often give low
Rfactors..


On Wed, 28 Feb 2024 at 16:21, Justin Cruite 
wrote:

> Thanks everyone,
>
> I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å dataset.
> The data was processed using autoProc and the staranisano mtz was used for
> MR. The completeness is only 38%. It could be that the Rfree and Rwork
> reflection sets are small because of this? What is the best way to check
> the number of reflections used for Rwork and Rfree? Is this dataset usable
> at all?
>
> Thanks!
>
> Justin
>
> On Wed, Feb 28, 2024 at 10:21 AM nicfoos  wrote:
>
>> Hello Justin,
>>
>> There is something weird in your results. You mention Rwork/Rfree of
>> 0.1837.
>> This means a pretty good refinement and also is very unusual to be
>> obtain for a resolution of 3.37.
>> Additionally you should not have Rfree = Rwork.
>> I suspect something wrong with you Rfree reflections sets. What size is
>> it ? Is your dataset complet ?
>> How did you cut the res. ?
>>
>> I hope this may help you.
>>
>> Nicolas
>>
>>
>>
>> On 2024-02-28 16:10, Justin Cruite wrote:
>> > Hi everyone,
>> >
>> > What does it mean if your Rwork and Rfree are exactly the same?
>> >
>> > I solved a 3.37 Å structure with Phaser-MR and immediately ran 10
>> > cycles of refinement with wxc = 0.1. Everything else at default. The
>> > Rwork and Rfree are both 0.1837. Is this bad?
>> >
>> > Thank you!
>> >
>> > Justin
>> >
>> > -
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Rwork and Rfree the same?

[Eleanor Dodson]

Well - it is extremely surprising! How many reflections are there in the
"work" set (Rwork) and the "free" set (Rfree)?
I suspect that somehow all the reflections are in both sets??

Eleanor

On Wed, 28 Feb 2024 at 15:11, Justin Cruite 
wrote:

> Hi everyone,
>
>
>
> What does it mean if your Rwork and Rfree are exactly the same?
>
>
>
> I solved a 3.37 Å structure with Phaser-MR and immediately ran 10 cycles
> of refinement with wxc = 0.1. Everything else at default. The Rwork and
> Rfree are both 0.1837. Is this bad?
>
>
>
> Thank you!
>
>
>
> Justin
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Difficult Molecular replacement

[Eleanor Dodson]

Hmm - that is pretty confident that the spacegroup for this cell is P2 21
21  (72.61 73.73 147.23 90 90 90 ..)
There are some strong reflections along the "a" axis

*From pointless log*
Lattice unit cell after reindexing: deviation 0.88 degrees
  72.61  73.73 147.23  90.00  90.00  90.00

$TABLE: Axial reflections, axis a (lattice frame) rotation axis order 2:
$GRAPHS:I/sigI vs. index, axis a, rotation axis order 2:N:1,4,5:
:I vs. index, axis a, rotation axis order 2:N:1,2:
 $$
   Index  I   sigII/sigI   I'/sigI   $$ $$
   1   3418163 20.96 20.17
   2   6470219 29.58 28.19
 *  3  11743396 29.64 29.32*
   4 14  4  3.84  0.00
  * 5335 12 27.74 27.69*
   6 13  4  3.57  1.14
   7130  6 20.55 20.47
   8 13  5  2.79  2.13
   9 24  7  3.30  2.94
  10114  8 13.86 13.69
  11 44  7  6.18  3.94
  12689 29 23.87 23.84
  14150 11 13.61  9.76
   *   15   2122 84 25.14 24.78*
  16   1362 55 24.57 23.77
  17 98 17  5.81  1.61
  18   2186 88 24.91 24.75
  19570 27 20.77 18.75
  20593 29 20.54 20.11
  21 54 17  3.22  2.49
  22 17 13  1.31  1.41
  23 10 12  0.84  0.83
  24 45 17  2.72  2.71
$$

The output is this - pointless has swapped the order cell dimensions - no
idea why! and adjusted the SG accordingly
 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
  73.7310  147.2260   72.6080   90.   90.   90.=20
 * Space group =3D 'P 21 21 2' (number 18)

But pointless works with this cell
   Unit Cell:   72.61   73.73  147.23   90.00   90.00   90.00

so one would expect the MR solution to be in SG P2 21 21

Do you have such a solution?
Eleanor



On Wed, 21 Feb 2024 at 18:05, Marco Bravo  wrote:

>
> https://www.dropbox.com/scl/fi/aqxm6s28mwbvufx5vkt4z/j7pointless.log?rlkey=075kia624ehmtzugnu5n8ymy0=0
>
> Here is a link to the pointless file , thank you for your help!
>
>



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement

[Eleanor Dodson]

Various (all depressing) possibilities..
You don’t say what the sequence ID to the models us

Your protein is flexible with poor fit to the available models. How well do
those overlap?
The bioinformatics tools in i2 give you pictures showing this. Look at them
and see if there are sensible places to divide models up for the search.

You have crystallised the wrong protein - not common but it does happen..
I use cco4i2 fir most things and there is a MR option there to use SINBAD .
That checks against the pdb whether there is a deposited structure that has
a) your point group and cell, then whether that model fits your data.

Next go back to the data processing. The ccp4i2 report needs to be read
carefully.
Is the data poor?
Inspect the graphs and warning messages..
What is the  Rmerge?
Are there bad batches? There is a graph showing the variation against
batch.. if there are wild variations you may need to exclude some batches..
It will suggest there might be twinning ,
look st the Wilson plot graphs .


Is there non- crystallographic translation? ( not harmful but if the
translation is (x,y,z=1/2) say then the space group selection is
problematic - the fact that all l=2n+1 ( used to suggest the soacegroup is
P2i2i21) might be caused by that translation..

Then how many copies of your protein can fit into the crystal lattice?
There is a task - “import sequence “ then another “define AU contents”. You
input sequence and experimental diffraction data and it tells you if one or
two or many molecules can fit. That is only a guesstimate but if the cell
can hold many copies the MR search will be more challenging.
If there could be several copies a self rotation function ( in ccp4i2 part
of the data processing folder) might tell you there is a dimer ? Trimer?
Etc .. but you say you expect a monomer..

The good news is that you have a solution with r factors below 0.5. Have
you tried rebuilding from that starting point? In some cases Buccaneer/
modelcraft can take that model, discard the worst defined bits and rebuild
the model. Not terribly likely to succeed with 2.8A data and a poor MR
solution but worth a try..

On Tue, 20 Feb 2024 at 01:30, Gong, Zhen  wrote:

> Hello Marco,
>
>
>
> I also feel that it might be due to the wrong space group because all the
> homologous models and alphafold model did not improve the R values. Make
> sure that you turn on “All possible in same pointgroup” when you run
> Phenix.Phaser-MR. I work with P212121 crystals a lot. Sometimes, if the
> diffraction quality was not good, the data will be indexed as P222, or
> P21212 etc, and sometimes even C2221. Try all possible in same pointgroup
> and see what happens. Good luck!
>
>
>
> Zhen
>
>
>
> *From: *CCP4 bulletin board  on behalf of Marco
> Bravo 
> *Date: *Monday, February 19, 2024 at 20:17
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *[EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement
>
> [You don't often get email from mbrav...@ucr.edu. Learn why this is
> important at https://aka.ms/LearnAboutSenderIdentification ]
>
> Hello Todd, I get the best solution for p22121 space group after MR with
> an LLG score of 640 from phaser. and the Rfree is .4748. However after MR
> refinement does not lower the Rfree and it appears to make the Rfree worse.
> The XDS software indicates that my best solution is P21 21 2. Often Phaser
> MR places the solution in P 21 21 2. The helicase is a superfamily 2
> helicase and is only monomeric. Its a 543aa long protein with a MW of
> 62Kda. It should have two RecA like domains at the core but the protein I
> have crystallized has a previously uncharacterized n-terminal domain
> responsible for tight single stranded DNA binding.  I have tried different
> space groups manually but that resulted in clashing. I will be frank I do
> need to work on my crystallography background as crystal lattices, space
> group, and self-rotaion functions are limited. Thank you so far for your
> help , I will try further trimming down my search model into separate
> domain and trying that in the meantime.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
>
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C02%7Czg2234%40CUMC.COLUMBIA.EDU%7C09755ea7318947460db808dc31b1a714%7Cb0002a9b0017404d97dc3d3bab09be81%7C0%7C0%7C638439886434663013%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=ZVA0GLUUac8WEJ%2BNxxEiGXi2Hr%2BLUin0BFJMV6NZf0M%3D=0
> 
>
> This message was issued to members of
> 

Re: [ccp4bb] Difficult Molecular replacement

[Eleanor Dodson]

Cant answer your question
"This might be a silly question, but I do not know the answer: After
refinement in P1 how do I distinguish which axis is crystallographic and
which one in non-crystallographic?"

Space group validation with Zanuda
[image: image.png]
CCP4
https://legacy.ccp4.ac.uk › newsletter48 › articles › zanuda
<https://legacy.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html>
The program Zanuda presented in this article was developed to automate the
validation of space group assignment in such circumstances. In addition,
the program ...



On Wed, 21 Feb 2024 at 15:40, Oganesyan, Vaheh <
vaheh.oganes...@astrazeneca.com> wrote:

> Hi All,
>
> Interesting discussion as I have a similar case. In my case molecular
> replacement solution can be found easily in P21, P212121, with very similar
> looking electron densities. However, R-factors remain relatively high (mid
> 30s). In P1 completeness suffers (75% completeness), maps look decent, R
> factors are in high 20's. Resolution limit is 1.9A with CC1/2 in high res.
> shell ~0.7.
> This might be a silly question, but I do not know the answer: After
> refinement in P1 how do I distinguish which axis is crystallographic and
> which one in non-crystallographic?
>
> Vaheh
> --
> *From:* CCP4 bulletin board  on behalf of Randy
> John Read 
> *Sent:* Wednesday, February 21, 2024 9:18 AM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* Re: [ccp4bb] Difficult Molecular replacement
>
> Hi,
>
> It’s possible the true space group is P2(1) with the b-axis unique, and
> that subset of true symmetry is found repeatedly with different incorrect
> backgrounds of other copies. But I think the easiest way to resolve this
> unambiguously is to solve in P1, and let that uncover the true symmetry.
>
> Best wishes,
>
> Randy
>
> > On 21 Feb 2024, at 13:56, Pedro Matias  wrote:
> >
> > But curiously, all the 4 best solutions correspond to a SG with a 21
> screw along b.
> > And amazingly none of the TF solutions is rejected due to clashes.
> > On 21/02/2024 12:20, Eleanor Dodson wrote:
> >> Lots of comments, but it would be easier to actually look at your
> integrated data!
> >> Some of the stats look a bit ropey -
> >> 621 reflections labelled as outliers by PHASER?
> >> Very anisotropic
> >> Moments go mad at the highest resolution..
> >>
> >> The good news - extremely strong signal from the rotation function
> means the model is probably a good one.
> >> Bad news - translation function results do not select a definitive
> solution..
> >> Possible reasons
> >> Unit Cell: 72.61 73.73 147.23 90.00 90.00 90.00
> >> Most likely data problems - a axis ~ = b axis so twinning is possible
> >>
> >> I could add more comments if either you could share the unmerged data,
> or at least a pointless logfile..
> >> Cheers Eleanor
> >>
> >>
> >>
> >>
> >>
> >> On Wed, 21 Feb 2024 at 11:06, Randy John Read  wrote:
> >> Hi Marco,
> >>
> >> To add to what Kay has said:
> >>
> >> The intensity moments from Phaser (between 1.5 and 2 for the second
> moments after correcting for anisotropy) are indicative of likely twinning.
> With the cell dimensions, it might be possible to have pseudomerohedral
> twinning in an orthorhombic space group, but given the lack of distinction
> among possible choices of orthorhombic spac group (noted by Kay), it seems
> much more likely that the true symmetry is lower and that you have
> pseudosymmetry combined with perfect twinning.
> >>
> >> Judging from the strong and unambiguous rotation peak, your model is
> clearly very good, so I think it would be easy to ask Phaser to solve this
> by looking for 4 copies in space group P1. You can get P1 data either by
> expanding the orthorhombic data to P1 or by re-merging the data in P1. If
> the merging statistics were good, that would indicate that any twinning
> would be close to perfect, so just expanding the data would be a reasonable
> choice. Alternatively, you have reasonable redundancy so merging in P1
> would be a plausible choice. I would probably go with expanding the data,
> figuring out from the MR solution what the real symmetry is, and then
> merging the data with that symmetry.
> >>
> >> Unless there are some other pathologies, I think the MR in P1 is very
> likely to give a clear answer (or maybe 2 answers related by the twin
> operator). It’s formally possible that you could have a different number of
> copies (e.g. 6 in the unit cell) if the true symmetry were monoclinic, so
> keep an ope

Re: [ccp4bb] Difficult Molecular replacement

[Eleanor Dodson]

Lots of comments, but it would be easier to actually look at your
integrated data!
Some of the stats look a bit ropey -
621 reflections labelled as outliers by PHASER?
Very anisotropic
Moments go mad at the highest resolution..

The good news - extremely strong signal from the rotation function means
the model is probably a good one.
Bad news - translation function results do not select a definitive
solution..
Possible reasons
Unit Cell:   72.61   73.73  147.23   90.00   90.00   90.00
Most likely data problems - a axis ~ = b axis so twinning is possible

I could add more comments if either you could share the unmerged data, or
at least a pointless logfile..
Cheers Eleanor





On Wed, 21 Feb 2024 at 11:06, Randy John Read  wrote:

> Hi Marco,
>
> To add to what Kay has said:
>
> The intensity moments from Phaser (between 1.5 and 2 for the second
> moments after correcting for anisotropy) are indicative of likely twinning.
> With the cell dimensions, it might be possible to have pseudomerohedral
> twinning in an orthorhombic space group, but given the lack of distinction
> among possible choices of orthorhombic spac group (noted by Kay), it seems
> much more likely that the true symmetry is lower and that you have
> pseudosymmetry combined with perfect twinning.
>
> Judging from the strong and unambiguous rotation peak, your model is
> clearly very good, so I think it would be easy to ask Phaser to solve this
> by looking for 4 copies in space group P1. You can get P1 data either by
> expanding the orthorhombic data to P1 or by re-merging the data in P1. If
> the merging statistics were good, that would indicate that any twinning
> would be close to perfect, so just expanding the data would be a reasonable
> choice. Alternatively, you have reasonable redundancy so merging in P1
> would be a plausible choice. I would probably go with expanding the data,
> figuring out from the MR solution what the real symmetry is, and then
> merging the data with that symmetry.
>
> Unless there are some other pathologies, I think the MR in P1 is very
> likely to give a clear answer (or maybe 2 answers related by the twin
> operator). It’s formally possible that you could have a different number of
> copies (e.g. 6 in the unit cell) if the true symmetry were monoclinic, so
> keep an open mind on that question. You could just try finding the largest
> domain from splitting the AlphaFold model (presumably the domain for which
> you sent the log file), work out the symmetry from that solution, and then
> run a job to search for all the domains in the right space group. It’s
> generally a good idea, by the way, to ask Phaser to look for everything you
> expect to find in one job, because it has built-in logic to predict the
> best search order but then update it on the basis of preliminary results.
>
> There are different ways to sort out the true symmetry from the MR
> solution, but within CCP4 the Zanuda procedure is a very effective choice.
>
> Get in touch if you have any difficulties following this procedure, and it
> would be great to let the BB know the outcome!
>
> Best wishes,
>
> Randy Read
>
> > On 21 Feb 2024, at 08:42, Kay Diederichs 
> wrote:
> >
> > Hi Marco:
> >
> > short comments (I sent you also a private mail):
> > - the stats in CORRECT.LP look ok, but I'd like to know what ISa is, and
> what the number of outliers is ("misfits"). Seeing the delta-CC1/2 stats as
> a function of frame number is also useful for judging e.g. the radiation
> damage - this is available from XDSGUI in the "statistics" tab. Another
> remark: SPOT_RANGE=1 11 in COLSPOT will sample reciprocal space poorly - I
> always use the first half of the DATA_RANGE as SPOT_RANGE, at a negligible
> cost in CPU time.
> > - the Phaser logfile shows that the rotation function (table at line
> 1344) has only a single solution, but the translation function (table at
> line 7028)  does not even allow to determine the space group - there is
> very little contrast difference between potential "solutions".
> >
> > Best wishes,
> > Kay
> >
> > On Tue, 20 Feb 2024 21:45:12 +, Marco Bravo 
> wrote:
> >
> >>
> https://www.dropbox.com/scl/fo/pmw9nisdmq53yir2jqcmu/h?rlkey=zaj6cnknkjgkowrzf0vrmqdyf=0
> >>
> >> Here is a link to my Molecular replacement and asymmetric unit contents
> logfiles.
> >>
> >> I ran Simple molecular replacement phaser MR through ccp4 cloud with my
> .mtz that was auto-processed at the ALS light source Beamline 831. I
> truncated my Alphaphold model into several domains as suggested and ran
> separate MR jobs. All of them are still running but one MR job for just one
> of the helicase domains finished and that is the molecular replacement job
> logfile i have posted.
> >>
> >> I also posted my Data collection output for the crystal in the dropbox
> file.
> >>
> >> I also attached my XDS.INP and XDSCONV.INP files for more
> troubleshooting help.
> >>
> >> Thank you all for helping me I hope this provides more information to
> help 

Re: [ccp4bb] i2run crank2 problem

[Eleanor Dodson]

Hmm - I can't help with the scripting question, but it solved easily from
the I2 interface?

This is run on a Mac.

CRANK2 called SHELX - found SE with weak signal..
Some difference between hand
It traced ALA - R factor 41%

Then BUCCANEER or MODELFIR quickly built and sequenced the rest..
Eleanor


On Thu, 15 Feb 2024 at 09:07, zx2...@connect.hku.hk 
wrote:

> Dear Colleagues,
>
> I hope this message finds you well. I am reaching out to inquire if anyone
> has experience with *running Crank2 using the CCP4i2 i2run command*.
> Unfortunately, I've encountered some difficulties and would greatly
> appreciate any guidance or advice.
>
> For context, I've attached the script and files utilized in my attempts.
> Specifically, I'm interested in understanding how to address the errors
> I've encountered and would like to know the minimum input requirements for
> successfully running this script.
>
> Below are the errors I've received:
>
>
> Error in wrapper crank2 0.02: -ERROR- crank2:0 Error in wrapper crank2
> 0.02::
> *Anomalous scattering coeficients could not be determined.  Please input
> them or the wavelength.*
>
> Traceback (most recent call last):
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
> line 41, in CallCrankFromCCP4i2
> raise
> RuntimeError: No active exception to reraise
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/script/crank2_script.py",
> line 466, in process
> crank2 = ccp4i2crank.CallCrankFromCCP4i2(self, inpfile=inpfile,
> defaults=defaults, rvapi_style=rvapi_style)
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
> line 43, in CallCrankFromCCP4i2
> raise error
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
> line 29, in CallCrankFromCCP4i2
> crank =
> parser.ParseAndRun(ccp4i2crank,defaults,rvapi_style=rvapi_style)
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/parse.py",
> line 58, in ParseAndRun
> crank_prep.Run()
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/process.py",
> line 1017, in Run
>
> self.RunPreprocess(rundir=rundir,clear_out=clearout,save=restore,*args,**kwargs)
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/manager.py",
> line 107, in RunPreprocess
> self.GetAnomScatCoefs()
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/manager.py",
> line 327, in GetAnomScatCoefs
> common.Error('Anomalous scattering coeficients could not be
> determined.  Please input them or the wavelength.')
>   File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/common.py",
> line 34, in Error
> raise CrankError(message)
> common.CrankError: Anomalous scattering coeficients could not be
> determined.  Please input them or the wavelength.
>
> I would be grateful for any insights or suggestions you might have
> regarding this issue. Thank you very much for your time and assistance.
>
> Best regards,
> Xin
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Coot SSM Superpose Problem

[Eleanor Dodson]

Isnt this what you want? output of CCP4I2 fitting buccaneer to the other..


On Fri, 16 Feb 2024 at 09:46, zx2...@connect.hku.hk 
wrote:

> Dear all,
>
> Following the advice provided by Paul and Yi Min, the "*Symm Shift
> Reference Chain Here*" function has proven successful!
>
> I am deeply grateful for your guidance.
>
> Best regards,
> Xin
> --
> *From:* zx2...@connect.hku.hk 
> *Sent:* 16 February 2024 17:26
> *To:* Paul Emsley 
> *Subject:* Re: [ccp4bb] Coot SSM Superpose Problem
>
> Dear Paul,
>
> I apologize for the confusion in my previous description. To clarify,
> there are actually 4 copies within a single ASU.
>
> Following your suggestion, I tried the "Symm Shift Reference Chain Here" ,
> and it worked successfully. I greatly appreciate your assistance.
>
> Thank you so much!
>
> Best regards,
> Xin
> --
> *From:* Paul Emsley 
> *Sent:* 16 February 2024 11:06
> *To:* zx2...@connect.hku.hk ; CCP4BB@JISCMAIL.AC.UK
> 
> *Subject:* Re: [ccp4bb] Coot SSM Superpose Problem
>
>
>
> On 16/02/2024 01:45, zx2...@connect.hku.hk wrote:
>
> Dear all,
>
> Hello Xin,
>
>
> I encountered an issue while attempting to calculate the RMSD between two
> PDB files (each containing 4 ASUs)
>
> do they really though?
>
>
> using the SSM Superpose tool in Coot. Unfortunately, the tool was unable
> to superpose all ASUs accurately.
>
>
> That's because you have mismatched bundles. It seem to me that you need
> some "Symm Shift Reference Chain Here" action.
>
>
> Paul.
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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 ###
 ###
 ###
 ### CCP4 8.0.017: csymmatchversion 0.3 : 13/07/09##
 ###
 User: eleanor  Run date: 16/ 2/2024 Run time: 10:43:46 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
235-242.
 as well as any specific reference in the program write-up.



pdbin   
/Users/eleanor/CCP4I2_PROJECTS/jim-24948v162/CCP4_JOBS/job_308/XYZIN_QUERY-coordinates.pdb
pdbin-ref   
/Users/eleanor/CCP4I2_PROJECTS/jim-24948v162/CCP4_JOBS/job_308/XYZIN_TARGET-coordinates.pdb
origin-hand
pdbout  
/Users/eleanor/CCP4I2_PROJECTS/jim-24948v162/CCP4_JOBS/job_309/309_jim-24948v162_xyzout_csymmatch.pdb

Reference molecule:
  Spacegroup: P 1 21 1
  Unit cell:  Cell (52.932,160.535,95.563,90, 95.91,90)
Moving molecule:
  Spacegroup: P 1 21 1
  Unit cell:  Cell ( 52.96,160.61, 95.61,90, 95.92,90)


 Change of hand  : NO
 Change of origin: uvw = (   0.5,  0.25, 0)

Chain: C1-  43 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0, 0)
  with normalised score:  0.557587
Chain: C   45- 100 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0, 0)
  with normalised score:  0.498482
Chain: C  102- 363 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0, 0)
  with normalised score:  0.610847
Chain: A5-  44 will be transformed as follows:
  Symmetry operator: -x, y+1/2, -z
  Lattice shift: uvw = ( 1,-1, 0)
  with normalised score:  0.593516
Chain: A   48-  96 will be transformed as follows:
  Symmetry operator: -x, y+1/2, -z
  Lattice shift: uvw = ( 1,-1, 0)
  with normalised score:  0.55637
Chain: A  100- 361 will be transformed as follows:
  Symmetry operator: -x, y+1/2, -z
  Lattice shift: uvw = ( 1,-1, 0)
  with normalised score:  0.622536
Chain: D1-  43 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0,-1)
  with normalised score:  0.615694
Chain: D   45-  46 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0,-1)
  with normalised score:  0.276082
Chain: D   48-  94 will be transformed as follows:
  Symmetry operator: x, y, z
  Lattice shift: uvw = ( 0, 0,-1)
  with normalised score:  0.540653
Chain: D  102- 360 will be transformed as 

Re: [ccp4bb] Truncate / ctruncate / moments of E etc.

[Eleanor Dodson]

That pxmaths document was put together by Maria Turkenburg, with a bit of
input from me long long ago, but then the theory hasn't changed much in
that time.
My old reference was Srinvasen  & Parthasarathy
>From crystallography in India..
Influential books by him and his associates (R. Srinivasan, S.
Parthasarathy) in 1970 and 1976 on methods of solving the phase problem and
crystallographic statistics, are also noteworthy.

On Wed, 14 Feb 2024 at 15:49, Winter, Graeme (DLSLtd,RAL,LSCI) <
6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:

> Thanks Ian, that is much more what I was looking for!
>
> I knew I had seen something like this a long time ago
>
> All the best Graeme
>
> On 14 Feb 2024, at 15:36, Ian Tickle  wrote:
>
> You don't often get email from ianj...@gmail.com. Learn why this is
> important 
>
> This has graphs: https://www.ccp4.ac.uk/html/pxmaths/bmg10.html .
>
> -- Ian
>
>
> On Wed, Feb 14, 2024 at 3:25 PM Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Absolutely! However
>>
>> "(ie. not mathematics-first)”
>>
>> I was thinking of something with more pictures and graphs in ;-)
>>
>> I had already sent that newsletter but felt it may be a bit heavy going
>> as a first introduction
>>
>> All the best Graeme
>>
>> On 14 Feb 2024, at 15:17, David Waterman  wrote:
>>
>> Norman Stein's article at the back of this newsletter is the one I like!
>> https://legacy.ccp4.ac.uk/newsletters/newsletter47/newsletter47.pdf
>>
>> -- David
>>
>>
>> On Wed, 14 Feb 2024 at 15:14, Winter, Graeme (DLSLtd,RAL,LSCI) <
>> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Good afternoon all,
>>>
>>> Chatting to someone and wanted to provide some pointers on how to
>>> interpret the moments of E from truncate or ctruncate, and realised that I
>>> don't have any good *references*​ for this to hand i.e. what I am
>>> looking for and why, and my google search didn't come up with much that was
>>> useful
>>>
>>> Those of us who have a few orbits under out belts picked up a lot of
>>> this from osmosis but if you are trying to explain to someone new it's a
>>> bit more tricky
>>>
>>> What have I missed? Where would you point people today to understand
>>> e.g. Wilson stats and suchlike, from a user perspective (ie. not
>>> mathematics-first)
>>>
>>> Thanks in advance for any pointers
>>>
>>> Graeme
>>>
>>>
>>> --
>>>
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Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Eleanor Dodson]

If I remember  for coefficients with FOM and a precise PHI calculated, A =
FOM*cos(phi) B = FOM*sin(phi) C=D=0

If you have a probability curve for PHI. 0 to 360  such as you get from
experimental phasing, A B C D mirror this bimodal curve better ..


On Fri, 9 Feb 2024 at 09:58, Nitin Kulhar <
9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear sir
>
> Thank you for clearing that. I checked back to see that HLC/D are
> invariably 0 for all reflections, with the non-zero HLA/B supposedly having
> been originated from the probability distribution of phases *calculated*
> by phaser. Hopefully, I have not misunderstood it.
>
> Thanks and regards
> Nitin Kulhar
>
> On Thu, Feb 8, 2024 at 9:07 PM Randy John Read  wrote:
>
>> Hi,
>>
>> Hendrickson-Lattman coefficients are just a way of storing phase
>> probability information, and they can come from different sources including
>> atomic models. Phaser puts in HL coefficients because they could be handy
>> under some circumstances for combining the phase information from
>> experimental phasing. You might notice that only A and B are non-zero for
>> the molecular replacement HL coefficients. That’s because the phase
>> probability distribution is unimodal for calculated phases, whereas it’s
>> generally bimodal for experimental phases (thus requiring more
>> coefficients).
>>
>> Best wishes,
>>
>> Randy Read
>>
>> > On 8 Feb 2024, at 14:32, Nitin Kulhar <
>> 9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:
>> >
>> > Dear all
>> >
>> > Is anomalous diffraction necessary for determining experimental phases
>> and the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?
>> >
>> > MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems
>> to be generating HLA/B/C/D coefficients from an x-ray diffraction dataset.
>> >
>> > Wavelength:
>> > 1.54179 Angstrom.
>> >
>> > Sample:
>> > •
>> > Protein-small molecule ligand complex crystal.
>> > • No anomalous scatterer in the protein, the ligand, or the
>> crystallization condition.
>> >
>> > Data reduction:
>> > Xtriage and aimless analyses did not indicate significant anomalous
>> signal.
>> >
>> > I would appreciate any help in understanding the reasons for these
>> observations.
>> >
>> > Thanks and regards
>> > Nitin Kulhar
>> > PhD student
>> > c/o Dr Rajakumara Eerappa
>> > Macromolecular Structural Biology Lab
>> > Department of Biotechnology
>> > Indian Institute of Technology Hyderabad
>> > Kandi, Sangareddy
>> > Telangana, India - 502284
>> >
>> > Disclaimer:- This footer text is to convey that this email is sent by
>> one of the users of IITH. So, do not mark it as SPAM.
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> -
>> Randy J. Read
>> Department of Haematology, University of Cambridge
>> Cambridge Institute for Medical Research Tel: +44 1223 336500
>> The Keith Peters Building
>> Hills Road   E-mail:
>> rj...@cam.ac.uk
>> Cambridge CB2 0XY, U.K.
>> www-structmed.cimr.cam.ac.uk
>>
>>
> Disclaimer:- This footer text is to convey that this email is sent by one
> of the users of IITH. So, do not mark it as SPAM.
>
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Re: [ccp4bb] Data reprocessing

[Eleanor Dodson]

Did you make the original deposition ? If so the pdb accepts
re-depositions...

If it was done by someone else I guess the courteous thing is to notify
them and maybe talk to the pdb- redo team?
Cheers Eleanor

On Sat, 27 Jan 2024 at 01:53, Lucas Souza 
wrote:

> Dear all,
>
> After auditing and reprocessing a deposited structure with clear
> processing mistakes (missing/wrong residues and ligands with evident
> density) prior to some analysis that are going to be published, what should
> be done? Re-deposit the structure with a "reprocess" flag? Reopen the PDB
> deposition and update the files? Or simply state in the publication that
> the data was reprocessed?
>
> I'm curious if there's a consensus on handling situations of this nature.
>
> Cheers,
> Lucas
> 
>
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[ccp4bb] MOLREP bug..

[Eleanor Dodson]

I give MOLREP am input mtz with space group R32:H or R32 or H32

(entered as R32:H)


But MOLREP claims the SG is


default_PST_limit : 0.250 of origin peak

   PST will not be used.

   If you like to use PST, use keyword PST = Y


 * Space group : H 3*

  No: 146 Sett:   2

  Cell: 185.735 185.735 112.709   90.00   90.00  120.00



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Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

[Eleanor Dodson]

THere must be  some error in the calculation of the CC - or you are over
optimistic about what constitutes a fit!
What does the COOT density fit show?
Eleanor

On Wed, 10 Jan 2024 at 09:54, Martyn Winn - STFC UKRI <
7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> wrote:

> You can also try the CCPEM list for more cryoEM-orientated advice
> https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting,
> refinement, validation tools.
>
>
>
> Certainly, the map doesn’t look 3A, unless you have filtered it for these
> pictures. The CC for the middle and C-terminal domains is not just low, but
> essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5.
> So I think you need to look again at the initial fitting.
>
>
>
> HTH
>
> Martyn
>
>
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Basil
> Greber
> *Sent:* 10 January 2024 08:12
> *To:* ccp4bb 
> *Subject:* Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM
> map.
>
>
>
> Are you confident that your 3 Å resolution is correct? The map in the
> picture you supplied looks more like 5 Å, and the model vs. map FSC at 0.5
> is apparently 20 Å (?).
>
>
>
> Basil
>
>
>
> Gesendet mit der mobilen Mail App
>
> Am 10.01.24 um 05:57 schrieb Ketul Saharan
>
> Von: "Ketul Saharan" 
> Datum: 10. Januar 2024
> An: CCP4BB@JISCMAIL.AC.UK
> Cc:
> Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.
>
> Dear CCP4 community,
>
> I am building a structure model from ~3.0 Å resolution cryo-EM map. The
> structure consists of seven chains, with each chain containing an N-,
> middle, and C-terminal domain. Although I attempted to directly fit the
> Alfa-fold model, it became evident that the protein exhibited some
> movement, leading to poor fitting of N-terminal. To improve the fitting, I
> segmented the alfa-fold model into two parts: i) the N-terminal and ii) the
> middle and C-terminal domain. These fragments were then fitted into the
> map. After a few rounds of refinement using coot and phenix, the model
> effectively fitted all seven chains.
>
> The refinement resulted in a model to map correlation (CC mask) of over
> 60% for the N-terminus. *However, even though the model appeared to fit
> well inside the map, particularly in the middle and C-terminus regions, the
> refining consistently resulted in a map to model correlation of 0%.*
>
> For your perusal, I have included the snapshot of the phenix refinement
> results, the correlation graph, and the fitted model within the map
> (displaying one chain out of seven).
>
> I am not able to figure out why the correlation is so poor even after fine
> fitting of model to map.
>
> Any support in resolving this issue would be much appreciated.
>
>
>
> Thank,
>
> Ketul Saharan
>
>
>
> --
>
> Ketul Saharan
>
> Senior Research Fellow (Ph.D. Scholar)
>
> Laboratory of Macromolecular Crystallography (Lab-8)
>
> Institute of Life Sciences
>
> Nalco Square, Chandrasekharpur
>
> Bhubaneswar – 751023
>
> Odisha State, INDIA
>
>
>
> Phone: +91 8708290889
>
> * 124.png
> [image:
> Image removed by sender.] *
>
> * correlation.tif
> [image:
> Image removed by sender.] *
>
> * map to model.tif
> [image:
> Image removed by sender.] *
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
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[ccp4bb] How do I restrain B values?

[Eleanor Dodson]

I thought it was possible to stop B values on bonded atoms from fluctuating
wildly?
But I am quite unable to follow the newly formatted documentation..



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Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Eleanor Dodson]

Hmmm -  I am not sure about the value of this - one expects the longer
floppier side chains to have very different B values for the CB than the
OE2..

The program BAVERAGE gives you a plot of mean B value residue by residue..



*baverage* - averages B over main and side chain atoms
SYNOPSIS¶ 
*baverage XYZIN* *foo_in.pdb* *RMSTAB* *foo_out1.tab* *XYZOUT*
*foo_out2.pdb*
[Keyworded input ]
DESCRIPTION¶ 

A very simple minded program to read a PDB file, tabulate to RMSTAB the
average B values residue by residue (main chain and side chain separately)
and the RMS deviation of the B values from this mean. It also outputs a PDB
file with outlying B factors reset to lie within the given range.

On Fri, 5 Jan 2024 at 03:08, chenzhonghao...@163.com <
chenzhonghao...@163.com> wrote:

> Dear CCP4 community,
>
>  I found that Refmac5 refined the temperature factor only by four modes
> (see the bottom of the attached figure). However, no
> grouped B-factor (one or two per residue instead of one per atom) was
> found.
>
>  Actually, PHENIX and CNS can do it. But we are not familiar with both
> software. I want to know whether Refmac5 refines one or
> two group B per residue (for side and main chains) grouped temperature
> factor?
>
>  Any help would be highly appreciated
>
>  Thanks in advance.
>
> best,
>
>
>  Zhonghao Chen
>
>
>
>
>
>
>
>
> 
>
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Re: [ccp4bb] Query on density fitting to phosphate

[Eleanor Dodson]

Back to the value of an anomalous map - IF the anomalous data is good
enough to give a significant peak at a sulphur position, you might expect
to get a peak at a well ordered phosphate- if no sulphur peaks  not much
hope...

On Mon, 25 Dec 2023 at 19:51, Tom Peat <
b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello Dale,
>
> Thank you for the correction/ clarification.
> I think this is still a tricky question, as in solution, this is an
> average state and one doesn't have a stable hydrogen (or two) sitting
> discretely on the phosphate. More specifically, the hydrogens are coming
> off and popping back on constantly (just the ratios change depending on the
> pH). It is likely that the phosphate is also moving in and out of the
> binding site of a protein in solution. What state is captured in a crystal
> structure and is that consistent across all of the proteins in that
> crystal?
> As you say, one needs very high resolution to determine the bond length
> difference between those oxygens with and without a potential hydrogen
> attached to orient a phosphate correctly in a structure, assuming that
> there is only a single preferred orientation to start with.
> I believe the original question was whether in fact the density supported
> a phosphate ion, and I still believe that looking for some anomalous signal
> may be a good way to approach that question.
> Nonetheless, I stand corrected and there is likely to be some hydrogen on
> phosphate ions found in crystal structures.
> Happy holidays to all, tom
> --
> *From:* Dale Tronrud 
> *Sent:* Monday, December 25, 2023 8:52 PM
> *To:* Tom Peat ; CCP4BB@JISCMAIL.AC.UK <
> CCP4BB@JISCMAIL.AC.UK>
> *Subject:* Re: [ccp4bb] Query on density fitting to phosphate
>
> [You don't often get email from de...@daletronrud.com. Learn why this is
> important at https://aka.ms/LearnAboutSenderIdentification ]
>
>
> Hi,
>
> I wanted to correct a statement by Prof. Peat about the ionic state
> of phosphate in solution.  Phosphate has four states differing by the
> number of attached hydrogen atoms.  The number of hydrogen atoms depends
> on the pH, or maybe it is the other way around since phosphate is used
> as a buffer.  I've attached a plot of the fraction of each species as a
> function of pH (Citation: "By Clarolux - Own work, CC BY-SA 4.0,
> https://commons.wikimedia.org/w/index.php?curid=90586171;).  There you
> can see that for all pH's usually seen in mother liquors the solution is
> almost completely either HPO4(-2) and H2PO4(-1).  A binding site may, of
> course, prefer a species that is present in low concentration but such a
> protein will be fighting entropy to fill its pocket.
>
> Unless your mother liquor has an extreme pH you should expect that
> the phosphate species you are seeing in your crystal has either one or
> two hydrogen atoms attached.  Their presence will affect both the nature
> of the hydrogen bonding of the protein to the phosphate and will change
> the length of the P-O bonds (with the P-O-H bond being about 0.05 A
> longer than the P=O bond).  The two lengths will only be distinguishable
> given very high resolution diffraction data but there are examples in
> the PDB where the differences are clear.  You can determine the presence
> of an hydrogen atom at much lower resolution if the hydrogen bond is
> made with an obligate hydrogen bond acceptor.
>
> The inappropriate identification of an ion as PO4(-3) will
> significantly degrade the quality of any electrostatic potential one
> calculates from the model.
>
> I did a quick-and-dirty search of the PDB for the various species of
> phosphates in PDB entries.  While I found 5979 models with PO4(-3) (ID:
> PO4) I only found 42 with HPO4(-2) (ID: PI) and 27 with H2PO4(-1) (ID:
> 2HP).  I didn't find any H3PO4 and could not find an ID code for that
> molecule.  (This search was done quite a while ago.)   I believe
> depositors are mostly assuming the ID PO4 indicates any protonation of a
> phosphate ion but that is not correct.  I am unaware of any ID that is
> defined as a phosphate ion with unknown protonation state.  To conform
> to the wwPDB standards a depositor must do their best, using the limited
> data available to them, to choose one species of phosphate when they
> identify the presence of one, but almost certainly that choice should
> not be PO4.
>
> As usual, just causing trouble,
> Dale E. Tronrud
>
> On 12/17/2023 1:05 PM, Tom Peat wrote:
> > Dear Arpita,
> >
> > The hydrogens on phosphate, just like sodium and potassium, will come
> > off the oxygens in water.
> > To be more explicit, you don't have mono- or di-hydrogen phosphate in
> > water (except transiently), you just have phosphate, depending somewhat
> > on the pH of course. At 2.5 Angstrom resolution, there is no way to
> > 'see' hydrogens with X-rays.
> > Depending on the wavelength you used for your data collection, you could
> > try doing an anomalous map and 

Re: [ccp4bb] [pe...@leadszone.live: CCP4 Study Weekend-2024] (fwd)

[Eleanor Dodson]

Well - are any of our names worth pricing?!
Very very suspect..
Eleanor

On Fri, 15 Dec 2023 at 14:41, Robbie Joosten 
wrote:

> Hotel booking scammers for instance.
>
> Cheers,
> Robbie
>
> On 15 Dec 2023 15:34, Frank von Delft  wrote:
>
> I mean, who'd actually want that list anyway?!
>
> On 15/12/2023 13:23, Gerard Bricogne wrote:
> > Dear all,
> >
> >   I just received this a moment ago, and it looks most suspicious.
> Can
> > any action be taken, other than warn people not to follow up?
> >
> >   Best wishes,
> >
> >  Gerard
> >
> > - Forwarded message from Pedro Noel  -
> >
> > Date: Fri, 15 Dec 2023 13:13:19 +
> > From: Pedro Noel 
> > Subject: CCP4 Study Weekend-2024
> > To: "g...@globalphasing.com" 
> >
> > Hi ,
> >
> > Would you be interested in acquiring the attendees list of "CCP4 Study
> Weekend 2024"
> >
> >
> >
> >   Each record constitutes details such as: Company Name, URL, Contact
> Name, Title, Verified Email Addresses, Contact Number, Physical Address
> etc.
> >
> >
> >
> > Let me know if your interest and I will revert back with pricing and
> other deliverables.
> >
> >
> > Regards,
> > Pedro Noel
> >
> > - End forwarded message -
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
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> 
>
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Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

[Eleanor Dodson]

Very very interesting analysis - Thankyou!

On Fri, 1 Dec 2023 at 18:01, Tom Terwilliger <
b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Roberto,
> Thanks for the link to the DeepMind site!  I hadn't seen that and now I
> read it and the paper that they link to.  It looks to me as though they are
> making significant progress on ligands, dna, rna, but that the program is
> not yet available, so I don't think it can be tested yet!
> All the best,
> Tom T
>
>
> On Fri, Dec 1, 2023 at 5:19 AM Roberto Steiner 
> wrote:
>
>> Great paper indeed!
>>
>> However quite significant progress seems to have been achieved with
>> ligands as well (and not only)…
>>
>> https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/
>> Has anyone in the community put this to the test?
>>
>>
>> Best wishes
>> Roberto
>>
>>
>> *Roberto A Steiner*
>> www.steinerlab.org
>> https://twitter.com/steiner_lab
>>
>> roberto.stei...@kcl.ac.uk
>> Randall Centre for Cell and Molecular Biophysics
>> Faculty of Life Sciences and Medicine
>> King's College London
>> Room 3.10A
>> New Hunt's House, Guy's Campus
>> SE1 1UL, London, UK
>> Phone 0044 20 78488216
>> Fax0044 20 78486435
>>
>> roberto.stei...@unipd.it
>> Dipartimento di Scienze Biomediche
>> Università degli Studi di Padova
>> 
>> Viale G. Colombo 3
>> 
>> 35131 Padova, Italia
>> Telefono 0039 049 8276409
>>
>> *Responses to emails are not expected outside of your normal working
>> hours.*
>>
>>
>>
>>
>>
>>
>>
>>
>> On 30 Nov 2023, at 22:35, Tom Terwilliger <
>> b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> You don't often get email from
>> b6116340b489-dmarc-requ...@jiscmail.ac.uk. Learn why this is
>> important 
>> Hi Structural biologist colleagues!
>>
>> Our article that helps you make the case that the experiment is still
>> very much needed is now out:
>>
>> https://www.nature.com/articles/s41592-023-02087-4
>>
>> "AlphaFold predictions are valuable hypotheses and accelerate but do not
>> replace experimental structure determination."  Nature Methods (2023)
>>
>> Also, here is a video on the Phenix Tutorials YouTube channel that
>> describes this analysis:  https://www.youtube.com/watch?v=ugMPYdPo8Bc
>>
>> (I hope you will be happy to see that you and your structural biology
>> colleagues get the credit for making AlphaFold possible at 2:35 in the
>> introduction of this video!  Keep up the fantastic structural biology work!)
>>
>> All the best,
>> Tom T
>> --
>> Thomas C Terwilliger
>> Laboratory Fellow, Los Alamos National Laboratory
>> Senior Scientist, New Mexico Consortium
>> 100 Entrada Dr, Los Alamos, NM 87544
>> 
>> Email: tterwilli...@newmexicoconsortium.org
>> Tel: 505-431-0010
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>>
>>
>
> --
> Thomas C Terwilliger
> Laboratory Fellow, Los Alamos National Laboratory
> Senior Scientist, New Mexico Consortium
> 100 Entrada Dr, Los Alamos, NM 87544
> 
> Email: tterwilli...@newmexicoconsortium.org
> Tel: 505-431-0010
>
>
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Re: [ccp4bb] Occupany refinement protocol amd best practices

[Eleanor Dodson]

Pavel has listed the papers that describe the underlying maths but unless
you have high resolution data (> 1.9A say?) unscrambling results from
occupancy plus B factor refinement is problematic to say the least..

Think about residues such as ARG or LYS where the termini are often
extremely wobbly - they are certainly in the crystal mix butt assigning a
single coordinate to those atoms is a bit of a lie..   However we do just
that thinking it is better to give some guidance to the community than to
assign OCC=0.0 .

It is a bit the same for your ligand problem.
I tend to start with both occs fixed to 0.5 and see what happens to be B
values - no ideal but it gives some feeling for the problem and you can
adjust the occupancies in the light of the first results. As Pavel says -
once you are reasonably close the an answer you can try the mathematical
approach..
Good luck Eleanor


On Thu, 23 Nov 2023 at 00:30, Pavel Afonine  wrote:

> Hi Matt,
>
> Im wondering about occupancy refinements - both what's going on under the
>> hood and what are best practices.
>>
>
> since you are quoting Phenix I suggest this bit of reading that is
> somewhat relevant to your questions:
>
> https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
> This documents 13 typical occupancy refinement scenarios and how they can
> be handled in Phenix.
>
>
>> In the example I have, there is a ligand found in two distinct, partially
>> overlapping sites that can be modeled is some confidence, but likely there
>> are very low occupancy additional poses that blurs the electron density.
>> The modeled poses are known from prior work, so even though there is
>> smearing we know the ligand is in the modeled conformation. After
>> perturbing the crystal these I am trying to decide what the best approach
>> is to get some sort of numerical occupancy value to describe the
>> distribution.
>>
>
> I apologize in advance for this trivial statement, but refinement +
> validation are the tools to answer your question.
> If you can model these poses with an atomic model and prove they match the
> experimental diffraction data ("The modeled poses are known from prior
> work" doesn't count in this regard), then you are all good! Depending on
> the size ration ligand:whole structure, R factors may or may not be useful
> quantifiers of the modeling choices. So your best bets may be local
> quantities, such as refined ligand group occupancy, flatness of Fo-Fc map
> (assessed as map values at atom positions), local map-model CC, etc. Try to
> challenge your modeling decisions by placing similar to expected answers
> but knowingly wrong models and see how that changes the fit/quality
> criteria -- that may give you a way to assess uncertainty.
>
> 1.  In Phenix, how is the occupancy number determined?
>
>
> Please refer to the paper I mentioned above, and let me know if you have
> additional questions.
>
>
>> Is there a real-space correlation between the experimental density and
>> the model(weighted to occ) that is optimized?
>
>
> Yes, but very indirectly through optimization of overall standard ML
> target function.
>
>
>>   How can this go wrong?
>
>
> It can go wrong in as many ways as the refinement target function has
> local minima, that is in many thousands ways!
>
>
>> I fear that the smearing and heterogenous nature will through the
>> refinement off (over or underfitting to periphery density rather than
>> hyper-localized position of the model)
>>
>
> That is a valid concern that is good to keep in mind but that is not a
> show-stopper!
>
>
>> 2.  Are there errors associated with the occupancy numbers?
>>
>
> Yes, like with any model refinable parameter. For some discussion please
> see:
>
> https://www.nature.com/articles/s41467-018-06957-w
>
>
>>
>> 3.  For my own testing, I did 5% increments and manually observed Fo-Fc
>> and 2Fo-Fc maps and selected a value that resulted in the lowest amount of
>> both positive and negative Fo-Fc peaks.  This is how we submitted the work
>> to journal but reviewer wants it to be automatically calculated.
>
>
> Above mentioned paper is now more relevant in light of this question! Yes,
> you can do manual sampling to get starting values (because the closer they
> are to the true values, the better chances refinement is successful), then
> do some refinement starting with these values.
>
> Good luck!
> Pavel
>
>
> --
>
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Re: [ccp4bb] low resolution data refinement

[Eleanor Dodson]

Q0. Echoing Randy - how accurate is your starting model - Xray structure at
resolution 1.5A or high quality EM or NMR??

Q1. Are the solutions the same? There is a CCP4 tool in ccp4i2 - Match my
model which will check this taking into account symmetry and origin shifts.



On Tue, 21 Nov 2023 at 14:51, Randy John Read  wrote:

> Hi,
>
> Whether or not you’ll get anything useful from a 4.3 A MR solution depends
> on your question — maybe you’re interested in something large-scale like
> complex formation or domain movement, in which case it could tell you
> something.
>
> In any case, it’s important to have a good starting model. Unless you have
> a higher-resolution crystal structure of the same protein, your best bet
> would be something like an AlphaFold model. Next, if you want to refine it,
> the structure will tend to get worse at that resolution unless you only
> allow it to change when required to agree with your data. There are tools
> for both Refmac and phenix.refine to use your good-quality starting model
> as a reference model, with local or torsion angle restraints, and you
> should be using these.
>
> Best wishes,
>
> Randy Read
>
> > On 21 Nov 2023, at 12:02, Yahui Liu  wrote:
> >
> > Dear all,
> > I got a protein crystal dataset of 4.3 A and would like to some the
> structure with MR.
> > Now I am suffering with the refinement. I used both Refmac and Phenix.
> >
> > Someone could give me a hand or  any suggestions?
> >
> > All the best
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building
> Hills Road   E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
>
> 
>
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Re: [ccp4bb] low resolution data refinement

[Eleanor Dodson]

Sorry - the simplest answer - is get higher resolution data!
But there are some improvements possible.
How clear is your MR solution.
What is the similarity between model and your sequence?
Etc.


On Tue, 21 Nov 2023 at 12:03, Yahui Liu  wrote:

> Dear all,
> I got a protein crystal dataset of 4.3 A and would like to some the
> structure with MR.
> Now I am suffering with the refinement. I used both Refmac and Phenix.
>
> Someone could give me a hand or  any suggestions?
>
> All the best
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Eleanor Dodson]

You seem pretty near to having solved your structure!
Ignoring the data problems..

Extra steps I might have used.
1) Self rotation function. (in CCP4I2 the task is under data analysis ..)
Does it suggest a NCS operator?
If so is this a two fold? which might mean you have a dimer..


2) Now you have a reasonable R factor try extending the resolution. the
refinement program will weight down the high resolution less reliable data
but the extra information might marginally improve the maps.

3) Use the calculated phases to run an anomalous map - REFMAC will produce
the appropriate coefficients and you can display the map in COOT.
Do a peaksearch and you should of course see the sites SHELX found..
But sometimes you get peaks over S atoms and that makes you pretty
confident that the sequence there is correct.



On Wed, 15 Nov 2023 at 10:42, Kay Diederichs 
wrote:

> Hello Devbrat,
>
> your project is difficult and there is no magic bullet to solve its
> problems. Your approach is good because it always pays off to process
> the data carefully.
> In this respect, let me make a few comments.
> 1) you don't say why you call the diffraction patterns "multi-lattice".
> What exactly do you mean by that? Non-merohedral
> twinning? How many lattices superimposed and visible on all frames? Can
> they be separately indexed by XDS
> (see https://wiki.uni-konstanz.de/xds/index.php/Indexing)?
> 2) "XDS processing" _is_ integrating; what AIMLESS does is called scaling.
> 3) what do you mean by "monomer NCS"? NCS implies two or more copies of
> the same molecule in the asymmetric unit.
> These copies often form dimers, trimers, tetramers, ... by making
> more-or-less strong and specific interactions.
> 4) you've advanced amazingly far and it sounds to me that with a
> combination of your refined MR model with the SAD data you
> should be able to improve your solution. Look up the MR-SAD pipeline (for
> SAD after MR and for model rebuilding using anomalous
> data) of Crank2.
>
> If you want me to take a look at your raw data, upload the best datasets
> (native and SeMet) to a cloud service and send me the link.
>
> Good luck,
> Kay
>
> On Tue, 14 Nov 2023 21:25:30 +0530, Devbrat Kumar 
> wrote:
>
> >Hello everyone,
> >
> >The issue with the crystal is its multi-lattice nature; even the truncated
> >protein, which has been crystallized, exhibits multi-lattice
> >characteristics (detectable only after XRD).
> >
> >I have multiple native and selenium datasets with similar unit cell
> >parameters. (One axis is excessively long.) The XRD images were processed
> >using XDS in the P2 spacegroup, with unit cell parameters as follows: a =
> >27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data
> were
> >integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In
> >CRANK2, the Estimation of Matthews coefficient (Program used: GCX)
> >suggested the presence of monomer NCS with a solvent content of 63.6%. The
> >FA estimation and substructure detection were performed by SHELXC, which
> >detected a very weak signal below 3.4 Å. Substructure determination was
> >carried out using SHELXD, yielding a maximum figure of merit of 27.8 after
> >640 trials and suggesting 11 atoms in the substructure with an occupancy
> of
> >at least 25%. Phasing and substructure refinement were conducted using the
> >BP3 program, resulting in an FOM of 0.2. During hand determination, the
> >programs suggested combined DM (density modification) FOM and phasing CLD
> >score for hand one as 6.0 and for hand two as 4.783375. The tool didn't
> >choose the hand because the value is less than the threshold. Density
> >modification with Fourier recycling suggests that the final FOM for hand
> >one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives the
> >R factor and Rfree factor as 0.4262 and 0.4912.
> >
> >One of the MR templates (model with balbes) works(For MR, Identity with
> the
> >PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7
> >Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). The
> R
> >& Rfree is not decreasing for the dataset. I have played with detector
> >distances for spot resolution, but at one pHi the spots have merged as a
> >single spot, while at 90 degrees will give us the streak of spots.
> >
> >Looking forward to hearing from you regarding dataset processing ideas for
> >multi-lattice crystals(Native & Se dataset) and structure solution
> strategy.
> >
> >Thank you.
> >Regards
> >Devbrat
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
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>
> 

Re: [ccp4bb] Mean B value in refmac5

[Eleanor Dodson]

Are there some atoms with occupancies < 1.0 ?
You would need to weight those Bs by occ

On Sun, 5 Nov 2023 at 11:34, Ian Tickle  wrote:

> The arithmetic mean B value from the structure as quoted everywhere is
> pretty meaningless anyway and 10 Ang.^2 either way is probably not
> significant. Let's say some waters or LYS side-chains or whatever have B =
> 1000 Ang.^2. That will bias the mean B upwards, but those atoms do not
> contribute significantly to the total scattering except at very low
> resolution and might as well not be there, so they should not be included
> in the mean. A better method would be to weight the mean by the scattering
> power at the resolution limit. That should more closely match the B value
> from the Wilson plot.
>
> Cheers
>
> Ian
>
>
> On Sun, 5 Nov 2023, 10:45 Qixu Cai,  wrote:
>
>> Dear all,
>>
>> I found that the "Mean B value (OVERALL, A**2)" reported by refmac5 in
>> the head region of pdb file is 62.76. However, I calculated the average B
>> value of all B factors from all atoms and the result is 67.7. What makes
>> the difference? The canonical restrained refinement mode was used in
>> refmac5. When we prepare the Table 1 of manuscript, which one is correct
>> for the "average B value"?
>>
>> Thanks and best regards,
>> Qixu Cai
>> Email: caiq...@gmail.com
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>
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Re: [ccp4bb] About model building

[Eleanor Dodson]

Hmmm - r 50% rather suspect..
do the MR solutions from phaser and molten agree?
Eleanor

On Mon, 6 Nov 2023 at 05:10, Sam Tang  wrote:

> Dear all
>
> Thanks for all the input. I will definitely try out in the coming couple
> of days. To provide more information:
> - the data was checked in Xtriage and no major pathology was found.
> Completeness was 99.2% with multiplicity of >13. Mean I/sigma(I) 18.8,
> CC1/2 for outer shell 0.902.
> - After one round of refinement, the R-factor was around 0.5, which looked
> reasonable given the incorrect B-chain was not removed and sequence
> deviations in chain A not yet rectified.
> - While I said Arp/warp failed to rebuild the model, it did return 3
> helices in chain A and one in chain B when I ran in the QuickFold mode
> (secondary structure tracing) later on. So I am going to start with the
> helix in chain B and see how further manual rebuild goes.
>
> Thanks again and I shall send an update for any progress.
>
> Kind regards
>
> Sam
>
>
> On Sun, 5 Nov 2023 at 06:26, Firdous Tarique 
> wrote:
>
>> Do the mass spec of your crystal to identify the other protein. Once done
>> solve your structure and build the complete model. This should be straight
>> forward and quick.
>>
>> Best Wishes
>>
>> On Sat, 4 Nov 2023, 09:05 Sam Tang,  wrote:
>>
>>> Dear community,
>>>
>>> I am solving the structure of a complex between proteins A and B, where
>>> A is a protein with known homologs and B is a novel protein isolated from
>>> plant. The diffraction data was at 1.9 Ang collected in-house, indexed to
>>> P321. Using A as the search model, we have got a reasonable solution where,
>>> after one round of refinement, the A chain fits the map pretty well. What's
>>> left was to extend the termini and fit a few rotamers.
>>>
>>> For protein B (B chain) I have tried the web version of ARP/wARP but the
>>> outcome was not really good. The model was not successfully built as
>>> indicated by low model completeness and score. The tricky thing may be that
>>> we do not have the complete sequence information of this protein B in-hand.
>>> (The other way round, we more or less wish to rely on the high resolution
>>> data to confirm its sequence.) What approach would you then recommend to
>>> build the B chain in this scenario?
>>>
>>> Thanks in advance and best regards,
>>>
>>> Sam
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>
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Re: [ccp4bb] About model building

[Eleanor Dodson]

IF your MR solution is correct ( ie r factor falls on refinement to 40%
say) and your protein A is roughly 50% of the complex, and IF your data is
good to 1.9A (assumed SG correct etc) I would do my best to correct any
obvious rebuilding needed for protein A, ( r factor should fall further if
this is done well) , then as others suggest fit an idealised  alpha helix
or two, then try rebuilding again with the best sequence you can derive fir
B. Once r factors in the 30-40% range you can often fit a “ val leu phe “
type sequence. I personally find this sort of challenge fun ! But maybe
others don’t...
Eleanor


On Sat, 4 Nov 2023 at 19:55, Randy John Read  wrote:

> Hi,
>
> At 1.9A resolution there should be lots of possibilities, depending on the
> details.
>
> You imply you have partial sequence information for chain B. Is there a
> genome for your plant or a relative of it? You could search for possible
> matches to your sequence, and then test all the AlphaFold models for the
> sequences that come up.
>
> When you say chain A has known homologues, what was the sequence identity
> of the homologue you used as a model? If it wasn’t pretty high, you may
> well be better off using an AlphaFold model of the correct sequence for A.
>
> Do you expect chain B to have helices or do you see helices in the map?
> Just adding some poly-Ala helices (which will tend to be locally very
> accurate if incomplete) will help to improve your phases. Arcimboldo would
> be a good tool for this, and you should also try it for completing from
> chain A.
>
> Do you have any anomalous scattering signal in your data? Even if it’s not
> enough to solve the structure, any signal can be exploited, using MR-SAD,
> to improve your phases and in particular reduce model bias in your map.
>
> Of course, other people have pointed out that you should make sure you can
> be confident in the MR solution. Also, you didn’t mentione whether there
> might be any issues in the data, like twinning. Presumably you would have
> mentioned if there was more than one copy of each protein in the a.u.
>
> Best wishes,
>
> Randy Read
>
> > On 4 Nov 2023, at 14:04, Sam Tang  wrote:
> >
> > Dear community,
> >
> > I am solving the structure of a complex between proteins A and B, where
> A is a protein with known homologs and B is a novel protein isolated from
> plant. The diffraction data was at 1.9 Ang collected in-house, indexed to
> P321. Using A as the search model, we have got a reasonable solution where,
> after one round of refinement, the A chain fits the map pretty well. What's
> left was to extend the termini and fit a few rotamers.
> >
> > For protein B (B chain) I have tried the web version of ARP/wARP but the
> outcome was not really good. The model was not successfully built as
> indicated by low model completeness and score. The tricky thing may be that
> we do not have the complete sequence information of this protein B in-hand.
> (The other way round, we more or less wish to rely on the high resolution
> data to confirm its sequence.) What approach would you then recommend to
> build the B chain in this scenario?
> >
> > Thanks in advance and best regards,
> >
> > Sam
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building
> Hills Road   E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
>
> 
>
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Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

[Eleanor Dodson]

We should all thank you mandar for stimulating our thinking and setting off
a thoughtful discussion!

This is perfectly publishable - st 2,6A placing water molecules is a bit
problematic and you will probably only see clearly the well ordered solvent
hence the lower average b factor.

Just a pointer for all contributors to the BB, it helps to give the
resolution of your data up front. Sensible comment is easier then..
Good luck with your writing up. Eleanor

On Fri, 3 Nov 2023 at 07:11, Mandar Bhutkar <
b29d954423ab-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all, I want to express my gratitude for all your valuable
> suggestions. I would like to apologize for any confusion that may have
> arisen regarding the R merge number. Please understand that I am relatively
> new to this field and have a basic understanding, which may sometimes lead
> to using layman's terms. I've updated the data refinement table for your
> reference. The values in parentheses pertain to the highest-resolution
> shell. I plan to implement the suggestions provided in the previous email.
> I've noticed that out of 124 water molecules, only 19 have a B-factor of 30
> or above. However, when I examine the difference map, it appears that the
> density for all 124 has been appropriately weighted. (Earlier, there was a
> distinction between green and blue densities, but after adding water, it's
> consistently blue.) You can refer to the attached images for contour levels
> from the refinement (1.0 rmsd) and difference map (2.5 rmsd).
>
> Previously, I attempted to manually fill in water densities, which
> unfortunately resulted in a higher R-free value. I will continue to work on
> the valuable suggestions provided by all of you. However, if I'm unable to
> improve the model further, I have a few queries:
>
> Is it necessary to include solvent B-factors in the refinement table? I've
> observed that many low-resolution structure articles do not provide this
> data.
> Is the data publishable? For instance, in 2018, PDB ID: 5YIG was published
> in EJMC.
> How can I justify the lower solvent B-factor?"
> I hope this revised version helps convey your message more clearly.
> Thank you.
>
> *Resolution range*
>
> 23.06–2.60 (2.72- 2.60)
>
> *Space group*
>
> *P *2 21 21
>
> *Unit cell dimensions: a b c (Å)*
>
> *α, β, γ (°)*
>
> 51.6  60.7 184.36
> 90  90   90
>
> *Completeness (%)*
>
> 99.6 (99.3)
>
> *R**merge* a
>
> 0.168 (0.372)
>
> *I/σ(I)*
>
> 7.3 (3.3)
>
> *CC(1/2)*
>
> 0.977 (0.773)
>
> *Refinement*
>
> *Reflections used in refinement*
>
> 10011
>
> *Reflections used for R-free*
>
> 924
>
> *R-workb*
>
> 0.231
>
> *R-freeb*
>
> 0.273
>
> *Wilson B-factor (Å)*
>
> 28.9
>
> *Number of non-hydrogen atoms*
>
> 4302
>
> *Macromolecules*
>
> 4086
>
> *Ligands*
>
> 94
>
> *Solvent*
>
> 124
>
> *Protein residues*
>
> 508
>
> *RMS (bonds) (Å)c*
>
> 0.01
>
> *RMS (angles) (˚) c*
>
> 1.89
>
> *Ramachandran Plot*
>
>
>
> *Favored (%)*
>
> 97.83
>
> *Allowed (%)*
>
> 1.38
>
> *Outliers (%)*
>
> 0.79
>
> *Average B-factor (Å)*
>
> 28.0
>
> *macromolecules (Å)*
>
> 28.65
>
> *ligands (Å)*
>
> 48.98
>
> *solvent (Å)*
>
> 18.44
>
> On Fri, Nov 3, 2023 at 2:44 AM Nicholas Clark <
> b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> This is why I said this is somewhat subjective.
>>
>> I would agree I/sigI of 0.6+ and cc1/2 of 0.5+
>> in high res shell is fine but these values are overall, as the resolution
>> range is 23-2.6 angstroms.
>>
>> On Thu, Nov 2, 2023 at 12:16 PM Eleanor Dodson <
>> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Am I confused? I would accept an I/SigI of 1+, and a CC1/2 of 0.5 as
>>> pretty acceptable?
>>> E
>>>
>>> On Thu, 2 Nov 2023 at 15:03, Dr. Kevin M Jude 
>>> wrote:
>>>
>>>> As suggested by the (conflicting) observations of Eleanor and Nicholas,
>>>> it’s not clear whether you are showing data collection statistics for the
>>>> full resolution range or just for the high resolution shell. If for the
>>>> whole dataset, your Rmerge, I/sigma, and CC1/2 are high, low, and low,
>>>> respectively; if for the high resolution shell, they suggest that you
>>>> should include higher resolution data in your refinement, if available.
>>>>
>>>>
>>>>
>>>> See https://doi.org/10.1107/S090744491361
>>>> <htt

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

[Eleanor Dodson]

Am I confused? I would accept an I/SigI of 1+, and a CC1/2 of 0.5 as pretty
acceptable?
E

On Thu, 2 Nov 2023 at 15:03, Dr. Kevin M Jude  wrote:

> As suggested by the (conflicting) observations of Eleanor and Nicholas,
> it’s not clear whether you are showing data collection statistics for the
> full resolution range or just for the high resolution shell. If for the
> whole dataset, your Rmerge, I/sigma, and CC1/2 are high, low, and low,
> respectively; if for the high resolution shell, they suggest that you
> should include higher resolution data in your refinement, if available.
>
>
>
> See https://doi.org/10.1107/S090744491361 and
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/, and for the
> standard format of reporting these statistics see any crystal structure
> reported in Acta Cryst D.
>
>
>
> Best wishes
>
> Kevin
>
>
>
> *From: *CCP4 bulletin board  on behalf of Mandar
> Bhutkar 
> *Date: *Thursday, November 2, 2023 at 12:34 AM
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *[ccp4bb] how to increase b factor for water in protein- ligand
> crystal structure
>
> Hi everyone,
>
> I am working on one of the x-ray diffraction data. Refinement details are
> given below. My solvent b factor is 18.44. Can anyone pls suggest me how to
> improve the data?
>
> Thank you.
>
> --
>
> Mr. Mandar Bhutkar,
>
> Ph.D. student,
>
> Molecular Virology lab,
>
> IIT Roorkee.
>
> *Resolution range*
>
> *23.06–2.60*
>
> *Space group*
>
> P 2 21 21
>
> *Unit cell dimensions: a b c (Å)*
>
> *α, β, γ (°)*
>
> 51.6  60.7 184.36
> 90  90   90
>
> *Completeness (%)*
>
> 99.3
>
> *Rmerge a*
>
> 0.372
>
> *I/σ(I)*
>
> 2.67
>
> *CC(1/2)*
>
> 0.773
>
> *Refinement*
>
> *Reflections used in refinement*
>
> 10011
>
> *Reflections used for R-free*
>
> 924
>
> *R-workb*
>
> 0.231
>
> *R-freeb*
>
> 0.273
>
> *Wilson B-factor (Å)*
>
> 28.9
>
> *Number of non-hydrogen atoms*
>
> 4302
>
> *Macromolecules*
>
> 4086
>
> *Ligands*
>
> 94
>
> *Solvent*
>
> 124
>
> *Protein residues*
>
> 508
>
> *RMS (bonds) (Å)c*
>
> 0.01
>
> *RMS (angles) (˚) c*
>
> 1.89
>
> *Ramachandran Plot*
>
>
>
> *Favored (%)*
>
> 97.83
>
> *Allowed (%)*
>
> 1.38
>
> *Outliers (%)*
>
> 0.79
>
> *Average B-factor (Å)*
>
> 28.0
>
> *macromolecules (Å)*
>
> 28.65
>
> *ligands (Å)*
>
> 48.98
>
> *solvent (Å)*
>
> 18.44
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
>
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Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

[Eleanor Dodson]

Well - you probably could use data to a higher resolution  I/SigI and CC
1/2 are quite high.
The better the resolution the better the model usually.

On the other hand your Rmerge is high-ish. Hard to comment without seeing
the data processing results. Look at the plots of 2nd moment, wilson plot,
Rmerge v Batch, and read the report carefu;ly.  Is there serious
radiation damage, should some batches be excluded etc, etc?
You may be able to check the anomalous difference maps to see if
"waters" are CL or some other metal ..

Good luck Eleanor

On Thu, 2 Nov 2023 at 08:14, Mark J. van Raaij 
wrote:

> Dear Mandar,
>
> - you may be able to find some more, less well-ordered, waters by looking
> at (difference) maps. These will probably refine to have higher B-factors,
> pushing your average up.
> - some of your best-ordered water molecules may in fact be metal ions, you
> can check the coordination. Modeling these as metal will then remove some
> waters with likely very low B-factors, also leading to a higher average
> B-factor for the remaining water molecules. Check My Metal may be useful:
> https://cmm.minorlab.org
>
> But:
> - it shouldn't really be a goal to increase the B-factor of the solvent,
> but to find and model all the water molecules (metal ions, protein and
> everything else) with reasonable density and hydrogen bonds.
> - when you write "improve the data", I assume you mean "improve the model".
>
> Best wishes,
>
> Mark
>
> Mark van Raaij
> Dpto de Estructura de Macromoleculas, lab 20B
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. +34 91 585 4616 (internal 432092)
>
>
> On 2 Nov 2023, at 08:24, Mandar Bhutkar <
> b29d954423ab-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi everyone,
> I am working on one of the x-ray diffraction data. Refinement details are
> given below. My solvent b factor is 18.44. Can anyone pls suggest me how to
> improve the data?
> Thank you.
> --
> Mr. Mandar Bhutkar,
> Ph.D. student,
> Molecular Virology lab,
> IIT Roorkee.
>
> Resolution range
>
> 23.06–2.60
>
> Space group
>
> P 2 21 21
>
> Unit cell dimensions: a b c (Å)
>
> α, β, γ (°)
>
> 51.6  60.7 184.36
> 90  90   90
>
> Completeness (%)
>
> 99.3
>
> Rmerge a
>
> 0.372
>
> I/σ(I)
>
> 2.67
>
> CC(1/2)
>
> 0.773
>
> Refinement
>
> Reflections used in refinement
>
> 10011
>
> Reflections used for R-free
>
> 924
>
> R-workb
>
> 0.231
>
> R-freeb
>
> 0.273
>
> Wilson B-factor (Å)
>
> 28.9
>
> Number of non-hydrogen atoms
>
> 4302
>
> Macromolecules
>
> 4086
>
> Ligands
>
> 94
>
> Solvent
>
> 124
>
> Protein residues
>
> 508
>
> RMS (bonds) (Å)c
>
> 0.01
>
> RMS (angles) (˚) c
>
> 1.89
>
> Ramachandran Plot
>
>
> Favored (%)
>
> 97.83
>
> Allowed (%)
>
> 1.38
>
> Outliers (%)
>
> 0.79
>
> Average B-factor (Å)
>
> 28.0
>
> macromolecules (Å)
>
> 28.65
>
> ligands (Å)
>
> 48.98
>
> solvent (Å)
>
> 18.44
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
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Re: [ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others

[Eleanor Dodson]

Hmm - I can give you scripts to use SHELX?
Eleanor

On Wed, 11 Oct 2023 at 11:02, fuxingke  wrote:

> Dear Colleagues,
>  Reacently, for SAD experiment, I find SOLVE and SHARP can refine the 
> variables
> of heavy atoms, such as occupancies, coordinates and thermal parameters.
> But how to use SOLVE and SHARP to refine heavy atom in command line in
> linux? I don't find a script to do it.
>  Who has the scripts template that implements the refinement of heavy
> atoms using SOLVE or SHARP or others? Could you please share them with me?
>
> Regards
>
>
>
> Best wishes,
>
> Fu Xingke
> Institute of Physics CAS
>
> --
>
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Re: [ccp4bb] Intractable outliers in wwPDB validation report

[Eleanor Dodson]

Well - some outliers are infix able! There are various reasons - floppy
residues like arg or lys
In multiple positions; strain due to protein folding constraints, etc.

I use the validation report to check for obvious modelling errors but if
you can’t find any, you have to just submit the results of your
experiment...

On Sat, 23 Sep 2023 at 02:29, Nitin Kulhar <
9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all
>
> We have refined (Refmac5) a crystallographic structure with Rw/Rf values
> 0.19/0.22 (Resln 2.67). However, the deposition has stalled on account of
> the wwPDB's preliminary validation report, which indicates map/model and
> geometry issues, with each criterion containing a few instances. We tried
> to correct these by varying overall geometry restraint weights, e.g.
> decreasing overall weights from default value of 1.0, incementally
> decreasing sigmas corresponding to the planarity restraint term. This did
> not resolve the issues.
>
> In another approach, real space refinement by hand (against 2fo-fc) in
> coot brought the geometry parameters within acceptable limits in addition
> to improved apparent agreement with electron density (2fo-fc, sigma=1), but
> uploading the resultant coordinates seems to undo the changes made in coot,
> as indicated by reappearance of same outliers in the subsequent validation
> report.
>
> I request your kind suggestions in this regard. Please also revert for any
> further information.
>
> Thanks
> Nitin Kulhar
> PhD student
> c/o Dr Rajakumara Eerappa
> Macromolecular Structural Biology Group
> Department of Biotechnology
> Indian Institute of Technology Hyderabad
> Kandi, Sangareddy
> Telangana, India 502284
>
> Disclaimer:- This footer text is to convey that this email is sent by one
> of the users of IITH. So, do not mark it as SPAM.
>
> --
>
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Re: [ccp4bb] the structures of Nucleic acid

[Eleanor Dodson]

I am afraid most scientists will use the most straightforward technique!
If SAD is available the PHOSPHATE backbone of DNA will provide sufficient
signal to allow SAD to work, and you get an unambiguous answer to whether
it is A-DNA or B or Z...
MR will usually work of course as well
Eleanor


On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan 
wrote:

> Dear Fu Xingke,
>
>  Depends on what Nucleic Acid you are talking of.  If it is RNA,
> you can expect some sequence to tertiary structure correspondence so you
> might be able to try more MR as compared to DNA.   DNA may have double
> helical architecture but less sequence to tertiary structure
> correspondence, and hence DNA is less likely to have a 3D structure like
> RNA specific structure for a sequence.
>
>  SAD has become a straight forward method to avoid all these
> problems to get ab-initio structure.  So many go for it directly.
>
> Hope that helps.
> Best wishes,
> Natesh
>
> On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:
>
>> Dear Colleagues,
>>  Reacently, I find the structures of Nucleic acid are solved by
>> single-wavelength anomalous diffraction(SAD). So, why molecular
>> replacement (MR) not?
>>
>> Regards
>>
>>
>>
>> Best wishes,
>>
>> Fu Xingke
>> Institute of Physics CAS
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
>
> --
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Associate Professor,
> School of Biology and Center for High-Performance Computing (CHPC),
> Founding and Current President of Cryo Electron Microscopy and 3
> Dimensional Image Processing Society of India (CEM3DIPSI),
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
>
> nat...@iisertvm.ac.in
> http://faculty.iisertvm.ac.in/natesh
>
> *Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
> *ORCID*: http://orcid.org/-0002-1145-5962
> Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
> *PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile
>
> Office Ph. 0091- 471-2778087
>
>
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>
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Re: [ccp4bb] Occupancy Refinement limitation

[Eleanor Dodson]

Low tech but simple.
Exclude both conformers from the refinement. (set occs to 0.00 so you still
see the coordinates in COOT)
Look at the difference map density and make a rough estimate of occupancy
from peak heights for a "fixed" bit of the conformers..

The relative ratios for different states should show up...
Eleanor

On Wed, 6 Sept 2023 at 11:49,  wrote:

> I would be tempted to try phenix.ensemble_refinement instead.
>
> Look at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949522/
> or
> https://phenix-online.org/phenixwebsite_static/mainsite/files/presentations/ensemble_refinement_burnley_at_al_10DEC2012.pdf
>
> or https://elifesciences.org/articles/00311
>
> Tassos
>
> On 6 Sep 2023, at 12:37, Matt Mcleod  wrote:
>
> Hi,
>
> I should be a bit more specific.
>
> We have many crystal structures to indicate that a loop adopts
> conformation A and conformation B, or - the loop can be disordered where
> the electron density is washed out.  These states are dependent on how we
> perturb the system.
>
> We have a series of data, as a function of osmolyte concentration, that
> adjusts this equilibrium and we want to put a numerical value onto it.
> Resolution is between 1.7 - 2.0 A. This is non-anomalous data but certainly
> would be helpful in the future to include if possible some anomalous
> scatters. Have been using phenix.refine.
>
> So what we have done is modeled both conformation A and B and are refining
> the data in order to get the occupancies (fixing B-factors) regardless of
> if there is electron density present for one of the two conformations since
> in some cases (likely all) there will be a population of both A, B, and
> disordered and the relative true occupancies will move.  I am trying to
> sort out how accurate these occupancy values are as opposed to showing the
> electron density for each conformation fit at some common threshold.  My
> general sense is that if it is modeled but no electron density, there will
> be a non-zero value and vice versa if it is the only conformation present
> it will be less than unity.
>
> I will take a look at the references!  Very much appreciated.
> Matt
>
> On Wed, 6 Sept 2023 at 02:08, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Well - occupancy refinement is particularly imprecise, and highly
>> correlated with temperature factors.
>> Also the population for a surface ARG or LYS may well have more than two
>> conformations, whereas some internal residue is better defined.
>> There is also the Q of solvent - dual occupancies will generate dual
>> solvent networks..
>>
>> ..You dont say what resolution your data are. Again at 0.8A you can be
>> confident - at 3A it is at best a guess. So I for one do not take the
>> numbers very seriously - they are a flag only.
>>
>> Presumably you didnt model the second conformation unless there was some
>> feature in an earlier map to suggest it existed?
>> Good luck Eleanor
>>
>>
>> On Wed, 6 Sept 2023 at 03:18, Pavel Afonine  wrote:
>>
>>> Hi Matt,
>>> I believe figure 3 here:
>>> https://www.nature.com/articles/s41467-018-06957-w
>>> is relevant to your question.
>>> Pavel
>>>
>>>
>>> On Tue, Sep 5, 2023 at 11:32 AM Matt McLeod 
>>> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am trying to get some insight in the accuracy/precision of occupancy
>>>> refinements.  I have done some 2-state occupancy refinements and have
>>>> observed the refinement achieving ~0.25-0.3 occupancy for the minor
>>>> population.  This population, when observing the electron density maps, had
>>>> essentially no evidence for it being present.  I was wondering:
>>>>
>>>> What are the errors in the reported occupancies?
>>>>
>>>> Is there a lower and upper limit to occupancy refinements?  As in, if
>>>> you occupancy refine two states and one is imaginary will it refine to
>>>> approximately 1 and 0?  Or does the background noise always given a
>>>> positive number to the imaginary set?  This would, to me at least, be the
>>>> lower and upper limits to the occupancy refinements and could be used as a
>>>> normalization factor for other atoms.  Maybe my logic is off...
>>>>
>>>> Any insight or literature would be appreciated!
>>>> Matt
>>>>
>>>> 
>>>>
>>>> To unsubscribe from the CCP4BB list, click the following link:
>&g

Re: [ccp4bb] Occupancy Refinement limitation

[Eleanor Dodson]

Well - occupancy refinement is particularly imprecise, and highly
correlated with temperature factors.
Also the population for a surface ARG or LYS may well have more than two
conformations, whereas some internal residue is better defined.
There is also the Q of solvent - dual occupancies will generate dual
solvent networks..

..You dont say what resolution your data are. Again at 0.8A you can be
confident - at 3A it is at best a guess. So I for one do not take the
numbers very seriously - they are a flag only.

Presumably you didnt model the second conformation unless there was some
feature in an earlier map to suggest it existed?
Good luck Eleanor


On Wed, 6 Sept 2023 at 03:18, Pavel Afonine  wrote:

> Hi Matt,
> I believe figure 3 here:
> https://www.nature.com/articles/s41467-018-06957-w
> is relevant to your question.
> Pavel
>
>
> On Tue, Sep 5, 2023 at 11:32 AM Matt McLeod  wrote:
>
>> Hi all,
>>
>> I am trying to get some insight in the accuracy/precision of occupancy
>> refinements.  I have done some 2-state occupancy refinements and have
>> observed the refinement achieving ~0.25-0.3 occupancy for the minor
>> population.  This population, when observing the electron density maps, had
>> essentially no evidence for it being present.  I was wondering:
>>
>> What are the errors in the reported occupancies?
>>
>> Is there a lower and upper limit to occupancy refinements?  As in, if you
>> occupancy refine two states and one is imaginary will it refine to
>> approximately 1 and 0?  Or does the background noise always given a
>> positive number to the imaginary set?  This would, to me at least, be the
>> lower and upper limits to the occupancy refinements and could be used as a
>> normalization factor for other atoms.  Maybe my logic is off...
>>
>> Any insight or literature would be appreciated!
>> Matt
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] New density quiz

[Eleanor Dodson]

I dont know what it is - but thats a beautiful map! What was in the
crystallisation pot, do you know?
Eleanor

On Tue, 29 Aug 2023 at 18:22, Bijelic, Aleksandar <
abae22057430-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear CCP4 members,
>
> I found the attached density in some of my structures and would highly
> appreciate suggestions what molecule this could be. The density is always
> located above an aromatic amino acid and close to the adjacent ASU (like in
> the attached picture). The mother liquid included MES/Tris as buffer,
> PEG8000 as precipitant, and ammonium sulfate as additive. Some tartrate
> "impurity" could also be included. My best guess currently is PEG. Looking
> forward to your suggestions.
>
> Cheers
> Aleks
>
>
>
> Von meinem/meiner Galaxy gesendet
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] An unknown but strong positive electron density in my crystal

[Eleanor Dodson]

THank you - it is on a two fold axis you said?
That means it could be a sort of average of a molecule..
Eleanor
PS Any anomalous peaks?



On Mon, 14 Aug 2023 at 10:32, Yue Li  wrote:

> Hi everyone,
>
> Thank you for your replies. I have uploaded the figures to a website. The
> link is here:
>
> yueliblog.webador.co.uk
>
>
> Best wishes,
> Yue
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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Re: [ccp4bb] An unknown but strong positive electron density in my crystal

[Eleanor Dodson]

Hmm - I cant see a picture..
Your email has this..
img
src="data:image/png;base64,iVBORw0KGgoNSUhEUgAAAq0AAAJPCAYAAABW0O0iAXNSR0IArs4c6QRnQU1BAACxjwv8YQUJcEhZcwAAFxEAABcRAcom8z8AAP+lSURBVHhe7P3nkzRJl92JVaXWWVlay0fL1lq+ql+t9Wg9mBmMBDEDDAEMFobdxYJL7tKMNO432n7hn+k8v+PhmZGRkVlZT/fb/XR3ltmxiozw8PBwce+51697rOkvrLDCCiv85rAe1lsbodo7DPXheVhvdEKls6X/vbC2vl6Sfi2sN4fG1Pn1alirtafPZVivK8/RrZhn8VpnO6xVqqGia5X2SOdUnmpD93RDtX8sHMW8C/d9HlDtq053HoT+o1+E1tm7odIaqp73QvPolXGaWv8gtG9


etc etc etc..

But have you checked the anomalous maps? They could help identify Calcium
say..

On Fri, 11 Aug 2023 at 14:28, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi
>
> > Has anyone seen similar density to this before and/or can suggest how to
> model this positive density? Many thanks.
>
> Romulan bird of prey?
>
> Harry
>
> >
> > Regards,
> >
> > Yue Li
> >
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
>
> 
>
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Re: [ccp4bb] High Temperature Factors with TLS

[Eleanor Dodson]

You need to tell us more details - is this a deposited structure?
Eleanor

On Wed, 2 Aug 2023 at 15:42, Thomas, Leonard M.  wrote:

> Hello All,
>
> A general questions though phenix.refine is being used for refinement.  A
> student I am working with has a structure that was solved and initially
> refined using TLS and NCS parameters.  They were given the structure to
> gain some experience in refinement and they have been asking me some
> questions, I was not involved in the initial work.  While everything seems
> to be happy and the model is correct with good refinement statistics for
> the most part one thing that I am unsure of is some of the heavier atoms
> (Phosphate and Sulfer) have very high temperature factors when looking at
> individual residues or ligands.  The temperature factors are at least twice
> as high as the lighter atoms they are associated with.
>
> I am at a loss to explain what is going on, I really have not used TLS
> refinement a lot so there is that.  Resolution is about 2.5 angstroms with
> good completeness.
>
> Thoughts?
>
> Thank You in advance
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Biomolecular Structure Core, Director
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmtho...@ou.edu
> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
>
>
> --
>
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Re: [ccp4bb] anomalous map in Coot - Linux vs. Win difference?

[Eleanor Dodson]

Hmmm -are the two ano maps contoured at the same level?
You can check this by setting the SCROLL option to the ano map.

The 2mFo-DFc maps look pretty identical..which suggests the two input mtz
files are similar.
You can get more information by viewing the inputs to make sure the values
are the same..
Eleanor


On Wed, 2 Aug 2023 at 13:53, Andrea Smith  wrote:

> Dear all,
>
> I used refmac in CCP4Cloud and then I opened the generated .pdb and .mtz
> from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot 0.9.6. I can
> see different anomalous maps in Coot and Wincoot - see attached printscreen
> where on the left there is a green electron density between the aspartates
> while on the right there is none. I tried to search if this is a bug but
> couldn't find info about this.
>
> Am I doing something wrong? Do I have a local software issue?
>
> Any advice would be appreciated, best,
> Andrea
>
> --
>
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Re: [ccp4bb] How to calculate experimental residual electron density map

[Eleanor Dodson]

You would hope it would show some hydrogen positions..
Eleanor

On Mon, 24 Jul 2023 at 13:47, Ankur Kumar Singh  wrote:

> Dear Prof. Eleanor Dodson,
> Thank you for the response. I will try generating difference map as told
> and will update.
>
> -
> Regards,
> Ankur K Singh
> Ph.D. Student
>
> ----------
> *From:* Eleanor Dodson 
> *Sent:* Monday, July 24, 2023 5:31 PM
> *To:* Ankur Kumar Singh 
> *Cc:* CCP4BB@jiscmail.ac.uk 
> *Subject:* Re: [ccp4bb] How to calculate experimental residual electron
> density map
>
> External Email
>
> hy not calculate structure factors without hydrogen atoms and look at the
> difference map?
> Eleanor
>
> On Mon, 24 Jul 2023 at 12:36, Ankur Kumar Singh <
> a8e375e16ee1-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear Members,
> I am trying to generate an experimental residual electron density map for
> a protein structure resolved at 1.1 Angstrom. One way to do this is by
> refining the structure using an aspherical model of charge distribution
> (Multipole density proposed by Hansen and Coppens) in MoPro. However, I
> cannot take that approach due to resolution limitation. Another way to
> calculate this map is-
>
>
>- Calculate only the atomic density for each atom in the structure.
>- Calculate the electron density for the entire structure which is
>2Fmo-dFc
>- Subtract these density to obtain the residual electron density map.
>
> Is this approach correct? Assuming it to be correct, I looked for CCP4
> tools to perform this job but I couldn't find it. Can anyone please suggest
> or comment on this?
>
> Thanks in advance.
>
> --
> Regards,
> Ankur K Singh
> Ph.D Student
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>



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Re: [ccp4bb] How to calculate experimental residual electron density map

[Eleanor Dodson]

hy not calculate structure factors without hydrogen atoms and look at the
difference map?
Eleanor

On Mon, 24 Jul 2023 at 12:36, Ankur Kumar Singh <
a8e375e16ee1-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Members,
> I am trying to generate an experimental residual electron density map for
> a protein structure resolved at 1.1 Angstrom. One way to do this is by
> refining the structure using an aspherical model of charge distribution
> (Multipole density proposed by Hansen and Coppens) in MoPro. However, I
> cannot take that approach due to resolution limitation. Another way to
> calculate this map is-
>
>
>- Calculate only the atomic density for each atom in the structure.
>- Calculate the electron density for the entire structure which is
>2Fmo-dFc
>- Subtract these density to obtain the residual electron density map.
>
> Is this approach correct? Assuming it to be correct, I looked for CCP4
> tools to perform this job but I couldn't find it. Can anyone please suggest
> or comment on this?
>
> Thanks in advance.
>
> --
> Regards,
> Ankur K Singh
> Ph.D Student
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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Re: [ccp4bb] How to deal with tNCS?

[Eleanor Dodson]

No attachments Lande Fu?
Your C2221 cell is pretty obviously related to the orthorhombic one.
(a b c )-C2221 ~  (2b 2c a)P212121
The cell volume of C2221 cell is ~ 4 x P212121 cell. -
8 symmetry related copies for C2221 and 4 for P212121
so if there are 2 molecules in P212121 ASU you expect 4 in the C2221 ASU.

I would reindex your P212121 cell as k l h
then change coordinates to Y,X,X ( or probably easier just run MR
again against the reindexed data)

Then place those coordinates in the C2221 cell, do a bit of refinement, and
look for the next pair.
I dont understand this "iFor fractional coordinate, it is 1/2 "..

Can you run MOLREP for the C2221 data set and send the log - phaser logs
are far too verbose!
Eleanor

On Fri, 21 Jul 2023 at 14:45, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello again, the R- and R-free are pretty high so there might be a problem
> with the space group or you may not have found all the molecules in the
> asymmetric unit. Are there big gaps in the packing with electron density to
> suggest additional molecules? Have you tried the option to input the
> current solution as a starting structure to see if the MR finds any more
> subunits. Is there any flexibility within your structure which could lead
> to domains having different orientations or visibility in your map? Can the
> model be split further into domains? The diffraction pattern does show a
> fair amount of splitting. MOSFLM might even be able to get additional
> lattices for you. I haven't done this stuff for a bit so others will know
> more about DIALS, etc ;-0 It would be good to see the results of twinning
> tests, if you have any. The one from CTRUNCATE, if you have it, is quite
> good.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 21 Jul 2023, 04:10, Lande <
> 8bc2565720d4-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
>  Dear Eleanor and Jon,
>
> Thank you for your replies. My good datasets are in P212121 space group
> and unit cell 56.67 60.53 67.51 90.00 90.00 90.00 ,2 copies in ASU. The
> tNCS one is in C2221 space group and unit cell 122.32 134.88  55.45  90.00
> 90.00  90.00. Matthews suggests 4 copies and I tried 4-6 copies to search
> in phaser (only 4 copies in solutions).  For fractional coordinate, it is
> 1/2 and the Rfree/Rwork is 0.4877/0.4466. This is another topic I can
> hardly found in modern crystallography textbooks..
>
> Here I also attached the self rotaion fuction. I guess there might be 8
> peaks but honestly I have no idea how to read those graphs. There is
> another screenshot of "more tNCS" image.
>
> Many thanks to your help.
>
> regards,
> Lande Fu
>
>
> --
>
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Re: [ccp4bb] How to deal with tNCS?

[Eleanor Dodson]

Well - it is hard to comment without more information, but many crystals do
have tNCS and yield perfectly satisfactory solutions..

How many molecules do you expect in the asymmetric unit? Look at
the Matthewscoefficient suggestions to guess that.
What are the fractional coordinates of the Patterson peaks? If they are
near 1/2, 1/3 etc they can cause whole classes of reflections to be
systematically weak and that guarantees higher R factors.

Do you also have non-crystallographic rtations (MOLREPs self rotation plot
is helpful here.. )
Anyway get back to us with more information if you like.
Eleanor


On Wed, 19 Jul 2023 at 15:46, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello Lande, the map which you have fitted looks quite good, as does the
> diffraction pattern. At that resolution it will benefit from anisotropic
> refinement, I think. What sort of R-and R-free do you have? You mentioned
> they are high with some of your solutions. What does the solvent content
> suggest for the number of molecules per asymmetric unit and have you found
> them all? With MR, there is usually a bewildering array of peaks with the
> same height, due to the high symmetry of the translation function. The
> programs will sort that out for you, usually. Is that what you mean with 48
> solutions? Are you sure of the space group? The main MR progs can try all
> possibilities, I think, so I assume you have done this. Also, my first and
> most memorable encounter with tNCS was with a crystal which had an NCS
> 2-fold parallel with a crystallographic 2(1) screw-axis. To my mind tNCS is
> just rotational NCS with a screw translation? Others will probably disagree
> ;-0
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 18 Jul 2023, 10:06, Lande <
> 8bc2565720d4-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> How to deal with tNCS? Dear all, I have read topics talking about tNCS
> problem a few years ago and have faced many tNCS data during my work.
> Generally, I just turned that tNCS button on in phaser during MR, and
> ignored high R/R-free if the MR solutions were correct. However, I always
> thought about what made tNCS to occur and what I can do further on tNCS
> data. Recently, I got sub 1.5A diffraction data of a simple protein (~100
> amino acid) soaking with a large ligand and it seems it suffers severe
> tNCS. It is very clear that two of its unit cell axis are doubled and there
> is many ghost density around the model. The other 10 datasets with
> different soaking time and concentration do not have tNCS, No ligand in
> there after modeling. So all my hope lays on that tNCS one. Here are my
> questions: 1. I know some proteins tend to form tNCS crystal but what
> causes tNCS in this crystal only? 2. In MR 48 solution were found and
> currently I have 4 copies in ASU. There seems to be more to fit the empty
> density. The map is messy and I cannot determinate the ligand status. What
> can I do now? Here I linked some screenshots. Any suggestions or articles
> to read will be helpful. Regards, Lande Fu
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Peculiar issue with C2 datasets

[Eleanor Dodson]

C2 Cell :



Average unit cell:   119.05   84.31  107.99   90.00   91.50   90.00

Space group: C 1 2 1


C2 shift ( if I have read your image correctly..)

60.32 2.137. 0.088 In fractions 60.32/119.05 2.137/84.31 0.00. = 0.504
0.023 0.00


See this site C121 has alt origin 1/2, ?,0 so your solutions A 7 B are more
or less equivalent.

(Molecular replacement programs are happy to select ANY origin..)

Maybe you needed to start your refinement from the original model by some
rigid body cycles to adjust for the 1/2A shift?


*See https://saf.bio.caltech.edu/hhmi_manuals/ccp4/alternate_origins.html
*

C 1 2 1 SG No: 5 (Standard short HM symbol: C2)

Number of alternate origins: *4*

This is a *polar spacegroup*: the origin is not fixed along the *B* axis
N*origin*XoYoZo
1 0. ?? 0.
2 0. ?? 0.5000
3 0.5000 ?? 0.
4 0.5000 ?? 0.5000

On Wed, 28 Jun 2023 at 10:14, Nichols, Charlie 
wrote:

> Hi,
>
>
>
> I am running an XChem / PanDDA based study and have collected ~2000
> datasets.
>
>
>
> ~100 of these behave anomalously and I am struggling to understand what is
> going on – any advice / comment appreciated (symmetry maths not my greatest
> strength )
>
>
>
> For manually processed datasets I am running Aimless via CCP4i GUI with
> ‘customised symmetry determination’ / ‘match index to reference’ and a
> previous hi-res dataset used as ‘reference MTZ’ so all datasets index
> consistently with the beta angle >90 solution.
>
>- Within XCE / PanDDA system auto-processed data are similarly
>re-indexed by Dimple to give a consistent population
>
>
>
> In most cases the hi-res model can then be refined against these data –
> solution-A
>
>
>
> With ~1 in 20 datasets however you get an Rfree of 30-45% but if you run
> Phaser and then refine then the Rfree drops to <25% - solution-B.
>
>
>
> Loading the two solutions into Coot shows solution-B appears to be a
> simple translation along the A-axis:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> SSM alignment output:
>
>
>
> In some cases, I have two crystals from the same drop soaked with the same
> ligand where one is ‘solution-A’ and the other ‘solution-B’
>
>
>
> Sample Aimless summaries pasted at end of this communication – B and C
> cell dimensions do vary a bit but there are solution-A datasets with
> greater shifts than observed between the sample datasets illustrated here.
>
>
>
> Are the two populations fundamentally different, or  is there a way to
> reindex the solution-B population so they can be included in the solution-A
> PanDDA runs?
>
>
>
> Thanks for your help,
>
> Take care, Charlie.
>
>
>
> (P.S. unable to share actual data due to client confidentiaility)
>
>
>
>
>
>
>
>
>
>
>
> *Aimless Summary – sample solution-A data*
>
>Overall  InnerShell  OuterShell
>
> Low resolution limit   68.11 68.11  2.49
>
> High resolution limit   2.40  8.98  2.40
>
>
>
> Rmerge  (within I+/I-) 0.082 0.057 0.734
>
> Rmerge  (all I+ and I-)0.094 0.067 0.877
>
> Rmeas (within I+/I-)   0.114 0.080 1.018
>
> Rmeas (all I+ & I-)0.113 0.082 1.056
>
> Rpim (within I+/I-)0.079 0.056 0.703
>
> Rpim (all I+ & I-) 0.063 0.047 0.581
>
> Rmerge in top intensity bin0.065- -
>
> Total number of observations  128856  2463 13718
>
> Total number unique40921   823  4270
>
> Mean((I)/sd(I))  5.9  15.2   0.9
>
> Mn(I) half-set correlation CC(1/2) 0.980 0.950 0.649
>
> Completeness99.9  99.7  99.7
>
> Multiplicity 3.1   3.0   3.2
>
> Mean(Chi^2) 0.66  0.77  0.54
>
>
>
> Anomalous completeness  90.6  92.7  90.9
>
> Anomalous multiplicity   1.5   1.7   1.6
>
> DelAnom correlation between half-sets -0.034-0.035-0.063
>
> Mid-Slope of Anom Normal Probability   0.780   - -
>
>
>
> The anomalous signal appears to be weak so anomalous flag was left OFF
>
>
>
> Estimates of resolution limits: overall
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  ==
> maximum resolution
>
>from Mn(I/sd) >  1.50: limit =  2.60A
>
>from Mn(I/sd) >  2.00: limit =  2.70A
>
>
>
> Estimates of resolution limits in reciprocal lattice directions:
>
>   Along0.99 a* + 0.15 c*
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.88A
>
>from Mn(I/sd) >  1.50: limit =  2.99A
>
>   Along k 

Re: [ccp4bb] Translational NCS (tNCS)

[Eleanor Dodson]

WELL - with such high LLG and translation NCSthe high R factors are a bit
surprising..
The Patterson info does not give the relative height of the origin peak to
the off origin one..
Questions which I would check.
Look at the data processing carefully. Are there bad batches? Could the
space group be wrong? Is the Wilson plot linear? Any twinning? etc..

How many molecules do you expect in the asymmetric unit?

And so on. I can look at your log files if you like and try to see if they
help.
Eleanor

On Tue, 27 Jun 2023 at 18:03, Muhammad Bashir Khan  wrote:

> Hello All;
>
> I have x-rays data of about 100 kDa protein at 3.3A. It gives MR
> statistics as LLG 150 and TFZ 7 but when I switched off the tNCS I got an
> LLG around 2500 and TFZ 45, but the R and Rfree are stuck at 39 and 43. The
> space group is 4. Any suggestion in this regard will be highly appreciated.
> Patterson's analysis is attached.
>
> Thank you all
>
> Bashir
>
> --
> --
> Muhammad Bashir Khan, Ph.D.
> Research Associate
> Department of Biochemistry
> Medical Science Bldg.
> Lab 3-27
> University of Alberta
> Edmonton AB, T6G 2H7
>
> Phone: 780-492-4577-
> e-mail: m...@ualberta.ca 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Script to refine water molecules - help

[Eleanor Dodson]

Wel - one way to do that is to use LABI FPART1=FS_from non-waters
PHIP1=PHIC_from non-waters.
You would need to split your model file into two - one containing the atoms
you want to fix, and the other the bits you want to refine.
Run 0 cycles of REFMAC to get an output with Fobs SIGFobs and FC PHIC from
the atoms you want to fix (0 cycles to prevent the protein moving towards
water positions)
Then refine the waters assigning LABI FP=..SIGFP=.. FPART1  and PHIP1

But I am not sure that is a very good idea? - there will be no restraint
terms between the atoms contributing to FPART and the waters
Good luck Eleanor


On Mon, 26 Jun 2023 at 21:44, De La Torre Marquez, Pedro Luis <
pedro_delatorremarq...@meei.harvard.edu> wrote:

> Thanks Eleanor.
>
> Yes, only refine waters.
>
> Best regards,
>
> Pedro
> ----------
> *From:* Eleanor Dodson 
> *Sent:* Monday, June 26, 2023 4:42 PM
> *To:* De La Torre Marquez, Pedro Luis <
> pedro_delatorremarq...@meei.harvard.edu>
> *Cc:* CCP4BB@jiscmail.ac.uk 
> *Subject:* Re: [ccp4bb] Script to refine water molecules - help
>
>
> External Email - Use Caution
>
> Do you mean only refine waters? In a general refinement run the waters
> will be refined along with protin/ligands etc..
> Eleanor
>
> On Mon, 26 Jun 2023 at 20:54, De La Torre Marquez, Pedro Luis <
> pedro_delatorremarq...@meei.harvard.edu> wrote:
>
> Dear all,
>
> I hope everything is going well.
> Back in 2019, I was using a script to refine all water molecules
> automatically during the refinement of an X-ray crystal structure. I no
> longer remember such script. Any suggestion?
>
> I will really appreciate it.
>
> Pedro.
>
> The information in this e-mail is intended only for the person to whom it
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Re: [ccp4bb] Script to refine water molecules - help

[Eleanor Dodson]

Do you mean only refine waters? In a general refinement run the waters will
be refined along with protin/ligands etc..
Eleanor

On Mon, 26 Jun 2023 at 20:54, De La Torre Marquez, Pedro Luis <
pedro_delatorremarq...@meei.harvard.edu> wrote:

> Dear all,
>
> I hope everything is going well.
> Back in 2019, I was using a script to refine all water molecules
> automatically during the refinement of an X-ray crystal structure. I no
> longer remember such script. Any suggestion?
>
> I will really appreciate it.
>
> Pedro.
>
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> https://www.massgeneralbrigham.org/complianceline .
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
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> --
>
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Re: [ccp4bb] British X-ray Crystallographers

[Eleanor Dodson]

Very interesting one from Katherine Lonsdale- thank you

On Thu, 25 May 2023 at 21:21, CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> I found these audio clips on the BBC website - might be of interest -
>
> https://www.bbc.co.uk/archive/dame_kathleen_lonsdale/z6v8kmn
>
> https://www.bbc.co.uk/archive/dorothy_hodgkin/zdhgbdm
>
>
> Harry
>
> On 24 May 2023, at 14:33, Frances C. Bernstein 
> wrote:
>
> Many years ago Shoshona Wodak told me that Word kept changing her name to
> Shoeshine Kodak!  At least Garmin is less typing to fix.
>
>   Frances
>
> On 2023-05-24 06:14, Elspeth Garman wrote:
>
> Thanks a lot Harry! Unfortunately there is only one of me so it should
> indeed be ‘man’ not ‘men’, although in these days of political correctness
> it should really be ‘Garperson’!
>
> Also Microsoft often changes it to ‘ Garmin’.
>
> Best wishes
>
> Elspeth
>
> Sent from my iPhone
>
> On 24 May 2023, at 10:56, Randy John Read  wrote:
>
> So have I! They’ll learn not to disrespect one of our favourite people.
>
> Randy
>
> On 24 May 2023, at 10:44, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi Gerard
>
> I’ve mentioned it to the organiser - we shall see how long the Garmen will
> be there!
>
> Harry
>
> On 24 May 2023, at 10:27, Gerard Bricogne  wrote:
>
> Dear Jon,
>
>  Quite a line-up indeed.
>
>  Might someone at the RSC correct the typo in Elspeth's surname (in two
>
> places)? Or is it a plural form ;-) ?
>
>  With best wishes,
>
>   Gerard
>
> --
>
> On Tue, May 23, 2023 at 10:16:54PM +, Jon Cooper wrote:
>
> I am biased, but this looks like an interesting meeting:
>
> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
>
> Best wishes, Jon Cooper.
>
> jon.b.coo...@protonmail.com
>
> Sent with [Proton Mail](https://proton.me/) secure email.
>
> 
>
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> 
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> 
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> -
>
> Randy J. Read
>
> Department of Haematology, University of Cambridge
>
> Cambridge Institute for Medical Research Tel: +44 1223 336500
>
> The Keith Peters Building
>
> Hills Road   E-mail:
> rj...@cam.ac.uk
>
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> 
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[ccp4bb] Obituary for Alexei Vagin for those who are interested

[Eleanor Dodson]

>From Louise Jones - Acta cryst editor

We put together an obituary for Alexei with contributions from his friends
and colleagues in Moscow and the UK

L*ouse says: I am hoping to put the obituary online this afternoon.*

*The page numbers have not yet been assigned but it can be cited with the*
*doi: Dodson, E. (2023). Acta Cryst. D79,*
https://doi.org/10.1107/S2059798323003364.
*The page numbers will be available at the end of the month.*

Best wishes
Louise



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Re: [ccp4bb] NCS consideration during refinement vis-a-vis ligand occupancy and flexible loops

[Eleanor Dodson]

As Robbie says, in such a case I just blindly refine with local NCS
restraints - this should improve the greater part of the model and thus
provide you with clearer maps. It is quite common for different copies of
the monomer to have differences - after all the crystal environment will be
different - but this should become clearer as refinement progresses. The
programs are pretty good at smudging out errors - B values usually go sky
high, and once you have a better map you can set the occupancies of the
poorly ordered bits to0.00 and see what, if anything comes back.
Eleanor

On Wed, 12 Apr 2023 at 10:27, Robbie Joosten 
wrote:

> The fact that your protomers have different density levels does not mean
> they are structurally different. The prior assumption should be that they
> are the same unless proven otherwise. So I would keep the (local!) NCS
> restraints in the initial stages and only remove them if it becomes
> apparent that this hurts refinement. No need to worry about the density
> averaging out. The models may average out but the density should still have
> enough signal to show any real differences.
>
> HTH,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Nitin
> > Kulhar
> > Sent: Wednesday, April 12, 2023 10:02
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] NCS consideration during refinement vis-a-vis ligand
> > occupancy and flexible loops
> >
> > Hello all
> >
> > I am writing to request opinions from the community regarding the
> following:
> >
> > Situation: An ASU comprising a non-crystallographic homo-octamer of a
> > biological monomer was obtained from MR. Electron density in the initial
> 2Fo-
> > Fc, as well as Fo-Fc maps, seems to vary widely* across the eight
> protomers for
> >
> > * the supposedly co-crystallized ligand (Kd ~100 micro-molar,
> determined
> > with ITC) and
> > * 1-2 flexible loops (too far from the ligand to interact with it
> directly)
> >
> >
> > Decision: Before commencing to do refinement in such a case, would it be
> > advisable to omit the flexible loops / binding site residues from the NCS
> > reference group to avoid inadvertently averaging out the density of
> structural
> > elements with partial occupancies (ligands and flexible loops)?
> >
> > * varying from non-existent in some protomers to huge unmodeled blobs in
> > others.
> >
> > Please write for any clarifications / further details. I would be highly
> grateful for
> > any help in this regard.
> >
> > Best regards.
> >
> > Nitin Kulhar
> >
> > PhD student
> > c/o Dr Rajakumara Eerappa
> > Macromolecular Structural Biology Group
> > Indian Institute of Technology Hyderabad
> > Kandi, Sangareddy
> > Telangana, India - 502285
> >
> > Disclaimer:- This footer text is to convey that this email is sent by
> one of the
> > users of IITH. So, do not mark it as SPAM.
> >
> >
> > 
> >
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>
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Re: [ccp4bb] new PDB file format

[Eleanor Dodson]

Ha ha!

On Sat, 1 Apr 2023 at 05:34, James Holton  wrote:

> Anyone who has ever had to lecture a student for writing their unit cell
> lengths to dozens of decimal places is going to love the new PDB
> format.  It is more compact, more realistic, and less misleading to the
> poor, downstream consumers of structural data.
>
> Only a few structures in the PDB are better than 1.0 A, and none come
> even close to 0.1 A.  Nevertheless, the classic PDB file format always
> listed atomic coordinates to three decimal places!  That's implying a
> precision of 0.001 A, which is not supported by the resolution of the
> data.  At long last, this age-old error is being corrected.  From now
> on, coordinates will be listed to the nearest Angstrom only.
>
> An unexpected consequence of this is that R-free of a typical structure
> is going to rise from the current ~20% to well into the 40%s.  This is,
> however, more consistent with high-impact structures published in
> big-named journals using modern, better data collection methods like
> XFELs and CryoEM, so we are going to call this an improvement.  Besides,
> R factors are just cosmetic anyway.
>
> Updated molprobity scores are not yet available while the authors fix
> bugs in their programs.  Right now, they return errors with the new,
> improved coordinates, such as:
> line 272: 57012 Segmentation fault  (core dumped)
>
> So, just as we all must adapt to Python 3 this new standard I'm sure
> will earn us all the thanks of future generations. They will no doubt be
> very grateful that we took these pains to protect them from the dangers
> of too many decimal places.
>
> -James Holton
> MAD Scientist
>
> 
>
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Re: [ccp4bb] Alexey Vagin

[Eleanor Dodson]

Alexei certainly contributed in MANY ways to Study Weekends!
Fun memories..
Eleanor

On Sun, 26 Mar 2023 at 20:00, Jurgen Bosch  wrote:

> Sorry to hear, he helped me a very long time ago during my PhD time when I
> was running into troubles with some of his programs.
>
> The York CCzp4 weekends were fun indeed, finishing off some wines tgat
> Paul Adam’s had stored away.
> Jürgen
>
> __
> Jürgen Bosch, PhD, MBA
> Center for Global Health & Diseases
> Case Western Reserve University
>
> https://www.linkedin.com/in/jubosch/
>
> CEO & Co-Founder at InterRayBio, LLC
>
> On Mar 26, 2023, at 14:40, James Foadi <
> 09daa8ec3774-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>  I am very sad to hear this! Alexey was one of my favourites when I was
> in York, and I have had many lovely conversations with him. You are right,
> Eugene, his contributions have helped and will keep helping many
> crystallographers and methods developers.
>
> May his soul rest in peace!
>
> James
>
>
> Sent from Yahoo Mail for iPhone
> 
>
> On Sunday, March 26, 2023, 7:29 pm, Eugene Krissinel - STFC UKRI <
> 6fcecdb9c847-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear All,
>
> It is with a great sadness that I share with you that Alexey Vagin passed
> away this Saturday in the Radcliffe Hospital in Oxford after suffering from
> a heart attack with subsequent complications. He was 78 years old.
>
> Alexey made many developments in methods and software for macromolecular
> crystallography, to which he devoted his whole life. He is known for his
> BLANC Suite for structure solution done at the Moscow Institute of
> Crystallography in the 1980s, as well as for his contributions to Refmac
> and Monomer Library. Many thousands of researchers have benefited from his
> work on Molrep and Balbes software for Molecular Replacement. After his
> retirement in 2010, Alexey developed and actively maintained the MorDA
> software for MR, which became a monument to his efforts.
>
> Alexey's work will continue to serve generations of researchers through
> his contributions to CCP4, where we will take the best care of his
> distinguished legacy.
>
> With sympathy to everyone who knew Alexey personally and for whom this is
> very sad news,
>
> Eugene
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
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Re: [ccp4bb] [i2dev] Alexey Vagin

[Eleanor Dodson]

Thank you Eugene for letting us know. He contributed so much to
crystallography, and was a good friend too.
MOLREP is such a well designed program, and he kept up his innovative ideas
- a true behind-the-scenes shaker and mover..
Eleanor

On Sun, 26 Mar 2023 at 19:29, 'Eugene Krissinel - STFC UKRI' via
ysbl-ccp4i2dev  wrote:

> Dear All,
>
> It is with a great sadness that I share with you that Alexey Vagin passed
> away this Saturday in the Radcliffe Hospital in Oxford after suffering from
> a heart attack with subsequent complications. He was 78 years old.
>
> Alexey made many developments in methods and software for macromolecular
> crystallography, to which he devoted his whole life. He is known for his
> BLANC Suite for structure solution done at the Moscow Institute of
> Crystallography in the 1980s, as well as for his contributions to Refmac
> and Monomer Library. Many thousands of researchers have benefited from his
> work on Molrep and Balbes software for Molecular Replacement. After his
> retirement in 2010, Alexey developed and actively maintained the MorDA
> software for MR, which became a monument to his efforts.
>
> Alexey's work will continue to serve generations of researchers through
> his contributions to CCP4, where we will take the best care of his
> distinguished legacy.
>
> With sympathy to everyone who knew Alexey personally and for whom this is
> very sad news,
>
> Eugene
>
> --
> CCP4i2 development & testing
> --
> Bug reports - core:
> https://fg.oisin.rc-harwell.ac.uk/tracker/?atid=169_id=92=browse
> Bug reports - interfaces:
> https://fg.oisin.rc-harwell.ac.uk/tracker/?atid=170_id=92=browse
> Find archived messages:
> https://groups.google.com/a/york.ac.uk/d/forum/ysbl-ccp4i2dev-group
>



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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Eleanor Dodson]

I am asked to test ZANADU which is meant to sort out spacegroup anomalies!
Maybe your example can be the test case..
Eleanor

On Fri, 24 Mar 2023 at 14:21, Gianluca Cioci  wrote:

> Hi Eleanor, Hi All,
>
> As suggested by Andrew (thanks!), I've switched off the NCS in Phaser and
> this gave a solution in C2 (a=66.2 b=83.9  c=66.2   90  98.7  90) that
> refines much better than the others (R=0.32/0.39).
>
> Still, I am not 100% convinced this is the correct cell/spacegroup... but
> it's a good starting point to continue the investigation.
>
> Thanks to all for your help !
>
> GIA
>
>
>
>
> Le 22/03/2023 à 07:10, Eleanor Dodson a écrit :
>
> You have tried all spacegroups within point groups? P2 p21 c222 c2221?.
>
> On Wed, 22 Mar 2023 at 03:01, Lijun Liu  wrote:
>
>> If data processing to be ok and all possible monoclinic and orthorombic
>> SG gave unreasonable high Rs, maybe good to give a try with p1 space group?
>>  Since the p-lattice indexing gave same a and  b also very close alpha
>> and beta, it could not exclude the possibility of p1 then twinned (also
>> together with ncs and tNCS) to show higher symmetry?
>>
>> Sent from my iPhone
>>
>> On Mar 21, 2023, at 1:25 PM, Jessica Bruhn 
>> wrote:
>>
>> 
>>
>> Hi Gianluca,
>>
>> Have you checked for diffraction anisotropy problems? It might be worth
>> running it through the STARANISO webserver:
>> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy
>> can make your data look twinned and elliptical truncation can help improve
>> maps.
>>
>> Good luck!
>>
>> Best,
>> Jessica
>>
>> On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
>> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Hello, can you give us a screenshot of a diffraction image, with the
>>> caveat that they never look all that good with fine-slicing, still it might
>>> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
>>> space groups.
>>>
>>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>>
>>> Sent from Proton Mail mobile
>>>
>>>
>>>
>>>  Original Message 
>>> On 21 Mar 2023, 16:43, Gianluca Cioci <
>>> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>
>>>
>>> Dear All,
>>>
>>> I have collected a dataset from a small protein diffracting at 2.7A
>>> resolution, here is the space-group determination from XDS:
>>>
>>>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>>>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>>>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>>>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>>>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>>>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>>>
>>> Clearly, something weird is going on...
>>>
>>> The structure can be solved in C2/P21/C2221 with different number of
>>> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>>>
>>> However the maps look bad and the structure is impossible to refine
>>> (Rfact > 0.5) in all the space-groups that I have tried so far...
>>>
>>> Thanks in advance for any advice on how to rescue these data !
>>>
>>> Cheers,
>>>
>>> GIA
>>>
>>>
>>> [image: Click to zoom the image]
>>>
>>>
>>> --
>>> Dr. Gianluca CIOCI
>>> Toulouse Biotechnology Institute 
>>> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
>>> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>>>
>>> Tel: +33 (0)5 61 55 97 68
>>> E-mail: ci...@insa-toulouse.fr
>>>
>>> TBI - INSA Toulouse135 avenue de Rangueil 
>>> <https://www.google.com/maps/search/135+avenue+de+Rangueil?entry=gmail=g>
>>> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Eleanor Dodson]

You have tried all spacegroups within point groups? P2 p21 c222 c2221?.

On Wed, 22 Mar 2023 at 03:01, Lijun Liu  wrote:

> If data processing to be ok and all possible monoclinic and orthorombic SG
> gave unreasonable high Rs, maybe good to give a try with p1 space group?  
> Since
> the p-lattice indexing gave same a and  b also very close alpha and beta,
> it could not exclude the possibility of p1 then twinned (also together with
> ncs and tNCS) to show higher symmetry?
>
> Sent from my iPhone
>
> On Mar 21, 2023, at 1:25 PM, Jessica Bruhn 
> wrote:
>
> 
>
> Hi Gianluca,
>
> Have you checked for diffraction anisotropy problems? It might be worth
> running it through the STARANISO webserver:
> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can
> make your data look twinned and elliptical truncation can help improve
> maps.
>
> Good luck!
>
> Best,
> Jessica
>
> On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, can you give us a screenshot of a diffraction image, with the
>> caveat that they never look all that good with fine-slicing, still it might
>> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
>> space groups.
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail mobile
>>
>>
>>
>>  Original Message 
>> On 21 Mar 2023, 16:43, Gianluca Cioci <
>> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Dear All,
>>
>> I have collected a dataset from a small protein diffracting at 2.7A
>> resolution, here is the space-group determination from XDS:
>>
>>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>>
>> Clearly, something weird is going on...
>>
>> The structure can be solved in C2/P21/C2221 with different number of
>> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>>
>> However the maps look bad and the structure is impossible to refine
>> (Rfact > 0.5) in all the space-groups that I have tried so far...
>>
>> Thanks in advance for any advice on how to rescue these data !
>>
>> Cheers,
>>
>> GIA
>>
>>
>> [image: Click to zoom the image]
>>
>>
>> --
>> Dr. Gianluca CIOCI
>> Toulouse Biotechnology Institute 
>> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
>> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>>
>> Tel: +33 (0)5 61 55 97 68
>> E-mail: ci...@insa-toulouse.fr
>>
>> TBI - INSA Toulouse135 avenue de Rangueil 
>> 
>> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> --
>>
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>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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>>
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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Eleanor Dodson]

cell   66.3   66.3   83.9  90.2  90.1  98.7.  P2 or P21 cell
Cell volume:364551.812

 Data line--- cell 86.4  100.6   83.9  90.0  90.2  90.0. Cell volume double
- C2 or C222 or C2221 cell
Cell volume:729240.938. ie

How many residues in your model?
It is hard to decide much without seeing the data..
Eleanor


On Tue, 21 Mar 2023 at 18:25, Jessica Bruhn  wrote:

> Hi Gianluca,
>
> Have you checked for diffraction anisotropy problems? It might be worth
> running it through the STARANISO webserver:
> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can
> make your data look twinned and elliptical truncation can help improve
> maps.
>
> Good luck!
>
> Best,
> Jessica
>
> On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, can you give us a screenshot of a diffraction image, with the
>> caveat that they never look all that good with fine-slicing, still it might
>> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
>> space groups.
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail mobile
>>
>>
>>
>>  Original Message 
>> On 21 Mar 2023, 16:43, Gianluca Cioci <
>> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Dear All,
>>
>> I have collected a dataset from a small protein diffracting at 2.7A
>> resolution, here is the space-group determination from XDS:
>>
>>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>>
>> Clearly, something weird is going on...
>>
>> The structure can be solved in C2/P21/C2221 with different number of
>> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>>
>> However the maps look bad and the structure is impossible to refine
>> (Rfact > 0.5) in all the space-groups that I have tried so far...
>>
>> Thanks in advance for any advice on how to rescue these data !
>>
>> Cheers,
>>
>> GIA
>>
>>
>> [image: Click to zoom the image]
>>
>>
>> --
>> Dr. Gianluca CIOCI
>> Toulouse Biotechnology Institute 
>> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
>> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>>
>> Tel: +33 (0)5 61 55 97 68
>> E-mail: ci...@insa-toulouse.fr
>>
>> TBI - INSA Toulouse
>> 135 avenue de Rangueil
>> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
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>>
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Re: [ccp4bb] To Trim or Not to To Trim

[Eleanor Dodson]

Thank you for such a careful analysis of modelling a "true" structure. You
should publish this James.

It shows amongst other things, how R factors depend on our modelling of
solvent which is not represented as individual atoms (And also I think on
how the scales are derived between observation and calculation.)
Years ago someone refined vitamin B12 against high resolution (0.6A?) data.
There is about 20-25% solvent volume I think..t was clear in the maps that
there were partially occupied networks of water which extended throughout
the lattice. This is probably true for proteins as well, and must affect
the conformations of surface sidechains?
Eleanor
The B12creference ...

Biophys J.  1986
Nov; 50(5): 967–980.
doi: 10.1016/S0006-3495(86)83537-8

PMCID: PMC1329821
PMID: 3790697 
Water structure in vitamin B12 coenzyme crystals. II. Structural
characteristics of the solvent networks.
H Savage 

On Sun, 19 Mar 2023 at 19:37, James Holton  wrote:

> They say one test is worth a thousand expert opinions, so I tried my hand
> at the former.
>
> The question is: what is the right way to treat disordered side chains?:
> a) omit atoms you cannot see
> b) build them, and set occupancy to zero
> c) build them, and "let the B factors take care of it"
> d) none of the above
>
> The answer, of course, is d).
>
> Oh, c'mon.  Yes, I know one of a,b, or c is what you've been doing your
> whole life. I do it too.  But, let's face it: none of these solutions are
> perfect.  So, the real question is not which one is "right", but which is
> the least wrong?
>
> We all know what is really going on: the side chain is flapping around. No
> doubt it spends most of its time in energetically reasonable but
> nevertheless numerous conformations.  There are 41 "Favorable" rotamers for
> Lys alone, and it doesn't take that many to spread the density thin enough
> to fall below the classical 1-sigma contour level. The atoms are still
> there, they are still contributing to the data, and they haven't gone far.
> So why don't we "just" model that?  Already, I can hear the cries of
> "over-fitting!" and "observations/parameters!", "model bias!", and "think
> of the children!"  Believe it or not, none of these are the major issue
> here. Allow me to demonstrate:
>
> Consider a simple case where we have a Lys side chain in ten conformers. I
> chose from popular rotamers, but evenly spread. That is, all 10 conformers
> have an occupancy of 0.10, and there is a 3-3-4 split of chi1 values
> between minus, plus and trans.  This will give the maximum contrast of
> density between CB and CG.  Let us further require that there is no strain
> in this ground-truth. No stretched bonds, no tortured angles, no clashes,
> etc.  Real molecules don't occupy such high-energy states unless they
> absolutely have to.  Let us further assume that the bulk solvent works the
> way phenix models it, which is a probe radius of 1.1 A for both ions and
> aliphatics and a shrink radius of 0.9.  But, instead of running one
> phenix.fmodel job, I ran ten: one for each conformer (A thru J).  To add
> some excitement, I moved the main chain ~0.2 A in a random direction for
> each conformer. I then took these ten calculated electron density maps
> (bulk solvent and all) and added them together to form the ground truth for
> the following trials. Before refinement, I added noise consistent with an
> I/sigma of 50 and cut the resolution at 2.0 A. Wilson B is 50:
>
> CCtrue   Rwork%  Rfree%   fo-fc(sigma)   description
> 0.8943 9.05   10.60  5.9 stump at CB
> 0.9540 9.29   11.73  6.0 single conformer, zero occupancy
> 0.947110.35   15.04  5.1 single conformer, full occupancy,
> refmac5
> 0.9523 9.78   15.61  4.9 single conformer, full occupancy,
> phenix.refine
>
> So, it would appear that the zero-occupancy choice "wins", but by the
> narrowest of margins.  Here CCtrue is the Pearson correlation coefficient
> between the ground-truth right-answer electron density and the 2fofc map
> resulting from the refinement.  Rwork and Rfree are the usual suspects, and
> fo-fc indicates the tallest peak in the difference map. Refinement was with
> refmac unless otherwise indicated. I think we often forget that both phenix
> and refmac restrain B factor values, not just through bonds but through
> space, and they use rather different algorithms. Refmac tries to make the
> histogram of B factors "look right", whereas phenix allows steeper
> gradients. I also ran all 10 correct rotamers separately and picked the one
> with the best CCtrue to show above. If you instead sort on Rfree (which you
> really shouldn't do), you get different bests, but they are not much better
> (as low as 10.5%).  So, the winner here depends 

Re: [ccp4bb] anomalous data usage

[Eleanor Dodson]

Oh dear - I didn’t mean to start this discussion - just to have a private
moan to Ian tickle, but there are some reasons for the regret.
First of all - column names had a meaning . For example a refmac hklout has
labels
f sigf  Phic from delfphwt etc and just occasionally one likes to see some
detail like  how fom falls off with resolution.

Then sometimes one has three data sets from “identical” crystals and it
would be nice to inspect how identical they are. cAD allows you to gather
them together with appropriate column names and I can find that useful.

Then there is the question of anomalous differences. We do much less
expensive phasing now where SAD or MAD datasets are important but I almost
always check the anom diff map at the end of refinement to make sure I
haven’t called SO4 a low bfacter water and that the MET residues really fo
have a SD atom.  Even when the anomsignal is insignificant these often show
up.

On Thu, 16 Mar 2023 at 09:00, Paul Bond <
30b0cd59fccb-dmarc-requ...@jiscmail.ac.uk> wrote:

> I believe there are many advantages to storing things *internally* as
> data objects with metadata instead of as columns of an MTZ file. How many
> students know what FP,SIGFP mean? And how many know that the FP,SIGFP
> columns in Refmac's HKLIN are not the same as the FP,SIGFP columns in
> HKLOUT? In an interface you can give these much more friendly names such as
> "observed amplitudes" and "amplitudes scaled by Refmac". The problem is
> that people should not need to access the *internal *i2 files to get to
> this data. Currently, you can export mini MTZs (containing only one data
> object) at the bottom of each report and you can export a full MTZ from
> Refmac using the Export MTZ button at the top of the interface, but
> probably this issue can be solved by doing the following:
>
>1. Making sure that reflection data objects have sensible names
>2. Expanding the "Export MTZ" functionality to have a customisable
>selection of any data objects (and allowing customisation of column labels
>as there may be clashes)
>
> Kind regards,
> Paul
>
> On Thu, 16 Mar 2023 at 07:14, Jan Dohnalek  wrote:
>
>> We are hitting the same problems also with students (so no rigidified
>> brains I think) ... the concept of "files" seems absolutely natural (also
>> to them) and when they ask about solving more tricky problems in i2 ... we
>> do the obvious, go back to ccp4i.
>>
>> I2 is fine when things are smooth and easy.
>>
>> Jan
>>
>>
>> On Wed, Mar 15, 2023 at 3:52 PM Randy John Read  wrote:
>>
>>> Hi Jon,
>>>
>>> My understanding of the philosophy is that new users would prefer to
>>> think about crystallographic data objects, rather than worrying about the
>>> arcana of MTZ files and the many different flavours of columns. There are
>>> tradeoffs — it can indeed be more difficult to find the bits of information
>>> you need, but you should be thinking in terms of the stored objects from
>>> the imports at the beginning of the project, rather than the files that
>>> hold them.
>>>
>>> Personally, I find multicolumn MTZ files easier to think about, but my
>>> brain probably rigidified a decade or two ago!
>>>
>>> Best wishes,
>>>
>>> Randy
>>>
>>> > On 15 Mar 2023, at 13:09, Jon Cooper <
>>> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> >
>>> > Hello Ian,
>>> >
>>> > if I understand you and Eleanor correctly, this is the philosophy of
>>> the mini-MTZ, i.e. if you are doing anything independent of i2, you have to
>>> dig around a bit to find which output file contains the columns you need.
>>> >
>>> > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>> >
>>> > Sent from Proton Mail mobile
>>> >
>>> >
>>> >
>>> >  Original Message 
>>> > On 13 Mar 2023, 23:27, Ian Tickle < ianj...@gmail.com> wrote:
>>> >
>>> >
>>> > Eleanor, which program is doing that and more to the point, why?
>>> >
>>> > -- Ian
>>> >
>>> >
>>> > On Mon, 13 Mar 2023 at 20:17, Eleanor Dodson <
>>> eleanor.dod...@york.ac.uk> wrote:
>>> > fIf you are using ccp4I2 for some forgotten reason the final output
>>> has one reflection with I+ and I-, another with Imean, another with Fmean -
>>> aagghh
>>> >
>>> >
>>> > On Mon, 13 Mar 2023 at 19:40, Ian Tickle  wrote:
>>> >
>

Re: [ccp4bb] anomalous data usage

[Eleanor Dodson]

fIf you are using ccp4I2 for some forgotten reason the final output has one
reflection with I+ and I-, another with Imean, another with Fmean - aagghh


On Mon, 13 Mar 2023 at 19:40, Ian Tickle  wrote:

>
> Hi Gottfried
>
> AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default.
>
> Cheers
>
> -- Ian
>
>
> On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried 
> wrote:
>
>> Dear all,
>>   I have a few questions handling (non) anomalous data:
>> By default aimless seems to produce Iplus and Iminus columns. Can I force
>> it to (also) create an Imean column?
>> What does refmac do, when it gets Iplus and Iminus (and their sigmas) as
>> input. Does it take only one of them or does it calculate and use Imean?
>> Greetings
>>   Gottfried
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] Structural alignment and classification

[Eleanor Dodson]

Does Superpose or GESAMT align multiple structures?
And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L
2 etc?
Eleanor

On Mon, 6 Mar 2023 at 14:53, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Or you could use Gesamt - also in CCP4.
>
> Harry
>
> > On 6 Mar 2023, at 13:15, Kay Diederichs 
> wrote:
> >
> > Dear Armando,
> >
> > besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign (
> https://zhanggroup.org/US-align/).
> > In my tests, THESEUS sometimes crashed in different ways. USalign is
> very robust; SUPERPOSE is fast.
> >
> > HTH,
> > Kay
> >
> > On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert 
> wrote:
> >
> >> Dear all,
> >> I want to align several structures we obtained from a fragment
> screening campaign and cluster them according to RMSD.
> >> Is MNYFIT still running? What else can I run?
> >> Thank you
> >> Armando
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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Re: [ccp4bb] Structural alignment and classification

[Eleanor Dodson]

See the answer last week  to my query about aligning nmr structures - use
Theseus .
I wonder if it could be used for this task too?
Eleanor

On Mon, 6 Mar 2023 at 07:35, Armando Albert  wrote:

> Dear all,
> I want to align several structures we obtained from a fragment screening
> campaign and cluster them according to RMSD.
> Is MNYFIT still running? What else can I run?
> Thank you
> Armando
>
> 
>
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[ccp4bb] NMR structires

[Eleanor Dodson]

I have been looking at 1hiq - an NMR structure with 20 models.
I had always assumed that an attempt had been made to overlap the first
with the second, third etc, but this does not seem to be so for this
structure..
Have I been labouring under a misapprehension?
Eleanor Dodson



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Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Eleanor Dodson]

Well - I made a copy of a ligand A 2001 and called it B 2001; gave each of
the "Ligands" occupancy 0.5, mangled the B molecule a bit and ran REFMAC .



It notes these atoms are too close but carries on refinement happily
enough..
But when I read the structure into COOT and try to refine the A copy say it
has a hissy fit and blows both copies out of the density...
This is  Coot version 0.9.8.7


  * From REFMAC log*

*Link info given in this sectoion is for information only*

*   If you want to use this links then either add them into the
pdb/mmcif file or use make link yes option*



* Status Link   Mon1  At1  alt1  ch1   res1  Mon2  At2  alt2  Ch2
 Res2   distM   distI*

*Unused  :.  LIG   C01   .  A 2001  LIG   C01   .  B
2001   0.599   1.524*

*Unused  :.  LIG   C01   .  A 2001  LIG   N02   .  B
2001   1.266   1.414*

*Unused  :.  LIG   C01   .  A 2001  LIG   C11   .  B
2001   1.863   1.507*

*Unused  :.  LIG   N02   .  A 2001  LIG   C01   .  B
2001   1.799   1.414*

*Unused  :.  LIG   N02   .  A 2001  LIG   N02   .  B
2001   0.398   1.304*

*Unused  :.  LIG   N02   .  A 2001  LIG   C11   .  B
2001   0.702   1.397*

*Unused  :.  LIG   C03   .  A 2001  LIG   N02   .  B
2001   1.287   1.397*

*Unused  :.  LIG   C03   .  A 2001  LIG   C03   .  B
2001   0.699   1.490*

*Unused  :.  LIG   C03   .  A 2001  LIG   C04   .  B
2001   1.313   1.490*



On Thu, 16 Feb 2023 at 17:25, Nigel Moriarty  wrote:

> Stuart
>
> The sum of occ in these three is 1.3 and it looks like you put the occ in
> the B-factor column.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Email : nwmoria...@lbl.gov
> Web  : CCI.LBL.gov
> ORCID : orcid.org/-0001-8857-9464
>
>
> On Thu, Feb 16, 2023 at 9:10 AM Stuart McQuarrie <
> 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Dear everyone that replied, thanks so much for the help thus far.
>>
>> Just for info I’m using Coot for Windows version 0.9.6 EL and
>> phenix.refine version 1.20rc4-4416-000
>>
>> RE Eleanor:  It appears my version of coot/refmac do not support separate
>> ligands in the same space at <0.5 occupancy. As an experiment, I tried
>> adding ATP and ADP at 0.45 occupancy to a different structure of mine. I’m
>> able to real space refine in coot (so both .cifs loaded successfully) until
>> I edit->merge the 2nd ligand and then the bonds look wrong and when I try
>> RSR it wants to force the ligand out and explodes the molecule.
>>
>> Original message: I thought that REFMAC tolerated dual occupancies if the
>> sum of the two conformers was <= 1.0?
>> Eleanor
>> Will test..
>>
>> RE Pavel: I tried following that as a guide, however I’m running into an
>> issue with restraints:
>>
>> I have made some progress troubleshooting the big cyclic molecule (ca6)
>> and products (pA3). I re-editted the pdb; gave them the altlocs ABC; made
>> sure they were same chain ID and residue number. However, when I try to
>> real space refine with coot I get the error:
>>
>> “No restraints found! Non-existent or minimal description of restrained
>> residues. Are you sure that you read a non-minimal mmCIF dictionary for
>> this monomer? Are you sure the PDB residue name matches the dictionary
>> residue name? If not, try File -> Import CIF dictionary. Alternatively, did
>> you check that the atom names of the PDB file match those of the
>> restraints? The residues in the chain are out of order. This can cause
>> problems with residues selection. Suggest you re-order residues in
>> increasing order.
>>
>> I definitely loaded the cifs. But it only allows me to rsr the ligand
>> with altloc A. If cA6 is A then I can only rsr cA6. If pA3 is A then I can
>> only refine pA3. When I delete->residue/monomer the cA6 with altloc A I can
>> suddenly rsr the pA3, so both libraries must have been loaded successfully
>> prior. I have included the snippet with the ligands just incase anyone
>> wants to see. Funnily enough phenix.refmac allowed me to refine with no
>> errors but it looks like it just ignored the pA3 as it did not properly fit
>> itself into the density the way ca6 did.
>>
>> Original Message:
>> Hi Stuart,
>> the answer, I think, is here:
>>
>> https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
>> Pavel
>>
>>
>> RE George: I added allow_duplicate_sequence_numbers() to my
>> coot-preferences but it didn’t seem to make a difference in my case. I
>> could already open 1EJG with no error. My issue now appears to be the
>> library file not recognising whichever ligand is not altloc A.
>>
>> Original Message:
>> Dear Stuart,
>> you have to add  allow_duplicate_sequence_numbers() to $HOME/.coot.py in
>> OSX or the appropriate place on Windows. For
>> Windows, as there is no $HOME, Coot uses .coot.py 

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Eleanor Dodson]

I thought that REFMAC tolerated dual occupancies if the sum of the two
conformers was <= 1.0?
Eleanor
Will test..

On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie <
974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:

> I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some
> refinement have noticed partial occupancy of it's hydrolysed form 2x A3,
> which has a cyclic 2'-3' phosphate on the terminal ribose.
>
> I tried fitting both ligands with 50% occupancy, but refinement doesn't
> allow them to occupy the same space.
>
> I subsequently tried text editing the pdb file, adding altloc identifiers
> to the ca6 and the 2 A3 molecules, making sure they were same chain and
> residue number as per this ccp4bb archive:
> http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html.
> However, before I refined I checked in coot and all the ligand atoms are
> scattered and disconnected.
>
> I have thought about using coot to generate an alt conformation of ca6 and
> then text editing the B conformation to be split and have a 2'-3' cyclic
> phosphate. I am not sure if this is the correct way because it is a
> different chemical structure, so I could use some advice.
>
> Kind regards,
> Stuart
>
> 
>
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Re: [ccp4bb] Renumber residues working PDB file - Applying a sequences numbering to PDB file

[Eleanor Dodson]

Usually you can bully coot into doing it but by bit. Say you need to
renumber A 1-8. I often have to change the chain id to Z say then renumber
Z. And so on . Then go back once you have finished and reset chain id fir
Z1-8 to A. Tedious but possible!

Or just run a few cycles of buccaneer with your structure - buccaneer
should do the job fir you...
Eleanor

On Sat, 4 Feb 2023 at 22:11, Matt McLeod  wrote:

> Hi all,
>
> I have been refining a structure and somehow along the way the residue
> numbers have completely shifted.  For instance, the first section of
> residues are shifted by say 8 numbers, then there is a gap from where the
> resnumbers go from 121, 151, 152, 153...and so on.  Its quite the mess.
>
> Is there a way to take a sequence file with residue numbers correct and
> apply these to the PDB file?  I have tried Renumber Residues in coot but
> this isnt working, it just shifts some of them and does opposite shifts
> elsewhere since its so discontinuous. Align and mutate just shifts them
> incorrectly from the inputted sequence without applying the sequence file
> number to the PDB.
>
> Any suggestions would be appreciated before I go and do this all
> manually...
> Matt
>
> 
>
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Re: [ccp4bb] Careless and negative Wilson B-factor

[Eleanor Dodson]

The tool must have sharpened your data - sometimes enhancing the outer data
does improve the electron density..
So I wouldnt worry about that "negative" B factor - it is doubtless a
result of the "careless" run, and not presumably the one you got at the
data processing step..
Eleanor


On Fri, 6 Jan 2023 at 08:27, "조규혁"  wrote:

> Dear all,
>
> I recently tested a novel merging tool for crystallography data called
> Careless (https://github.com/rs-station/careless).
>
> When I used it on our 2.6 A-resolution structure in the I23 space group
> with a lipid bound structure, I noticed that the electron density
> surrounding the acyl chain was significantly improved.
>
> However, I am concerned about the Wilson B-factor. The Phenix.table_one
> tool reports that the Wilson B-factor of the merged mtz file is -0.91.
> Phenix.Xtriage warns that a negative Wilson B-factor can be an indication
> of unusual pathology or artificial manipulation.
>
> Has anyone else encountered similar conditions? Are there any
> circumstances in which a negative Wilson B-factor can be rationalized?
>
> Thank you,
> Gyuhyeok
>
>
> P.S. Here is the part of the output of Phenix.table_one.
>
>
> Wavelength 1.
> Resolution range 37.98 - 2.60
> (2.69 - 2.60)
> Space group I 2 3
> Unit cell 161.128 161.128 161.128
> 90 90 90
> Total reflections 886846 (79364)
> Unique reflections 21520 (2135)
> Multiplicity 41.2 (37.2)
> Completeness (%) 99.95 (100.00)
> Mean I/sigma(I)
>
> 14.2 (0.8)
> * Wilson B-factor* *-0.91*
> R-merge 0.240 (4.566)
> R-meas 0.243 (4.629)
> R-pim 0.038 (0.757)
> CC1/2 0.998 (0.362)
> CC* 0.999 (0.729)
>
>
>
>
>
> PhD student
>
> Department of Chemistry
>
> Gwangju Institute of Science and Technology (GIST)
> 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005
>
> Republic of Korea
>
> Tel. +82 62-715-4633
>
> e-mail: gyuhyeok...@gist.ac.kr
>
>
>
>
> --
>
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Re: [ccp4bb] A challenging MR problem

[Eleanor Dodson]

I would start with coot. As bostjan suggests - 1) choose whole chain as a
fragment.
2) fit that over chain 2 and change its label to that of chain 2. (Remember
to make this a a copy of your fragment..)
3) check is there any density for the missing bit?

Then repeat till you have the whole thing.
And then merge all the pieces.

Of course your missing domain may be disordered. The twinning is suspicious.

And are you sure you have the right spacegroup?. 16 copies makes me suspect
there is more symmetry than you are using,






fit whole chain over chain 2.

On Wed, 9 Nov 2022 at 23:12, Bostjan Kobe  wrote:

> Superimposing that molecule on all the others?
>
>
>
> Bostjan
>
>
>
> --
>
> Bostjan Kobe *FAA*
>
> Australian Laureate Fellow
> Professor of Structural Biology
> School of Chemistry and Molecular Biosciences
>
> and Institute for Molecular Bioscience (Division of Chemistry and
> Structural Biology) and Australian Infectious Diseases Research Centre
>
> Cooper Road
> University of Queensland
> Brisbane, Queensland 4072
> Australia
> Phone: +61 7 3365 2132
> Fax: +61 7 3365 4699
> E-mail: b.k...@uq.edu.au
> URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
> Office: Building 76 Room 329
> Notice: If you receive this e-mail by mistake, please notify me, and do
> not make any use of its contents. I do not waive any privilege,
> confidentiality or copyright associated with it. Unless stated otherwise,
> this e-mail represents only the views of the Sender and not the views of
> The University of Queensland.
>
>
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of
> Medhanjali DasGupta 
> *Reply to: *Medhanjali DasGupta 
> *Date: *Thursday, 10 November 2022 at 9:05 am
> *To: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *Re: [ccp4bb] A challenging MR problem
>
>
>
> The data resolution is 2A.
>
> I have 16 chains in my model  out of which only one of the chains has the
> "missing" domain modeled. Is there a way to do MR to predict where the
> missing domains will go in the rest of the chains, based on my
> solved structure?
>
>
>
> Thanks for all the helpful suggestions!!
>
>
>
> M
>
>
>
> On Wed, Nov 9, 2022 at 3:11 PM Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Well you could just try the buccaneer pipeline. It would use the phases
> from your solved domain and try to fit the missing sequence. What are your
> twin fractions? And what is the resolution?
>
> Eleanor
>
>
>
> On Wed, 9 Nov 2022 at 21:06, Tim Gruene  wrote:
>
> Dear Medhanjali DasGupta,
> unless the resolution is really poor, the quickest try would be shelxe,
> starting from what you already have. It might work at, say, 2.8A
> resolution or better...
>
> Best,
> Tim
>
> On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali
> DasGupta  wrote:
>
> > Hello!
> > My protein structure has a missing domain and I am trying to figure
> > out the best way to model this missing domain using the solved
> > (modeled) fixed core domain? My data is also imperfectly twinned,
> > with 4 twin fractions according to refmac5.
> >
> >  Any help/ idea is appreciated!
> >
> >
> >
>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
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>
>
> --
>
> Thanks,
>
> Medhanjali Dasgupta
>
> Postdoctoral Research Scientist
>
> Lawrence Berkeley National Laboratory
>
> [image: Image removed by sender.]
>
>
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Re: [ccp4bb] A challenging MR problem

[Eleanor Dodson]

Well you could just try the buccaneer pipeline. It would use the phases
from your solved domain and try to fit the missing sequence. What are your
twin fractions? And what is the resolution?
Eleanor

On Wed, 9 Nov 2022 at 21:06, Tim Gruene  wrote:

> Dear Medhanjali DasGupta,
> unless the resolution is really poor, the quickest try would be shelxe,
> starting from what you already have. It might work at, say, 2.8A
> resolution or better...
>
> Best,
> Tim
>
> On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali
> DasGupta  wrote:
>
> > Hello!
> > My protein structure has a missing domain and I am trying to figure
> > out the best way to model this missing domain using the solved
> > (modeled) fixed core domain? My data is also imperfectly twinned,
> > with 4 twin fractions according to refmac5.
> >
> >  Any help/ idea is appreciated!
> >
> >
> >
>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
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Re: [ccp4bb] Low resolution and high anisotropy

[Eleanor Dodson]

How to deal with poor data is a challenge. Look at the images - see at what
resolution there is detectable diffraction.
Then run a self rotation function.Do you expect a trimer? dimer? etc and
does the self rotation give any clues?
Are your models dimers? trimers? etc.
Eleanor

On Wed, 26 Oct 2022 at 08:09, Lande Fu <
8bc2565720d4-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello Shenyuan,
>
>
> I noticed STARANISO processd the data all the way down to 1.7A, with very
> poor stats on high resolution shell. I have two suggesstions:
> 1.You may want to reivse the raw images to check the anisotropy (that all
> spots are distributed in an flat ellipse).
> 2. If you can  scale the data with Aimless suite in CCP4, check
> "Anisotropic deltaB" value below summary table.
>
>
> For MR, there is too much to tell and it's better to improve data
> processing first.
>
>
>
>
>
> regards,
> Lande
>
> 
>
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Re: [ccp4bb] Two Questions About SHELX

[Eleanor Dodson]

   - Those reflections are equivalent:
   - P6/mmm
   - reflections h,k,l k,-h-k,l -h-k,l.  all due to 3 fold
   - hkl equiv to -h,-k,l because of 6 foldnes

h,k,l equiv to k,h,-l. due to t extra 2 fold

So -1,3,1.  3,-2,1 and -2,-1,1 equiv
Also 1,-3,1  -3,2,1.   2,1,1

Etc.. etc
OK?

Eleanor



   - All *P6i2*:
   (h,k,l) already equivalent to (-h,-k,l) *and* (k,h,-l) *and* (-k,-h,-l)
   so we do not need to check.

>From CCP4 documentation on equivalent indices

On Thu, 13 Oct 2022 at 09:41, fuxingke  wrote:

> Dear Colleagues,
> Recently, I meet two problems during using CCP4:
> Fist, I used SHELX C to calculate 'Fa HKL' file.  I find 'H' , 'K'
> or 'L' sometimes are negative in 'Fa HKL' file for different spacegroup,
> But the 'H' , 'K' and 'L' are positive in 'inputing MTZ' file. Why  do 'H'
> , 'K' or 'L' become negative in 'Fa HKL' file sometimes? My test case is
> “20110112RH2-2long-ano-scale.mtz” file, the spacegroup of which is P6122.
> second, I want to covert 'Fa hkl' file to 'mtz file' using
> 'convert to/modify/extend MTZ' in 'Reflection Data Utilities' in CCP4. But
> I find the reflections 'H K L'  the resulting 'MTZ file' are not
> equivalent to these in inputing 'hkl file' when 'H' , 'K' or 'L' are negative
> in inputing 'hkl file'. My test case is '
> 20110112RH2-2long-ano-scale_shelx_fa5.hkl', and the spcacegroup is P6122.
> For example, for first reflection (-1, 3 ,1), I get (2, 1, 1) in resulting
> MTZ. But reflection (-1, 3, 1) is not equivalent to reflection (2, 1, 1)
> for spacegroup P6122. I don't know why and how to solve it ?
>
> --
>
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[ccp4bb] Anisotropy

[Eleanor Dodson]

There have been several discussions lately where anisotropy has been an
issue.
I have always believed weak unreliable data does little harm to refinement
or maps because it is given a very low weight in any calculation.
Weighting, in REFMAC anyway. is set partly using the Rfree  for that
resolution shell.
However if the data is anisotropic would be better if those weights were
based on shells constructed taking the anisotropy into consideration?

Or does it matter, and how could it be tested!

Eleanor



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Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

[Eleanor Dodson]

Dear Matt,
Your data past 2.5A is awfully weak, and wont contribute much to any map
you calculate. Each term at the outer resolution will have a very low
weight.
I sometimes cling to the belief that the weak data may help the B factor
refinement, but there isnt much evidence of that. There is a feeling that
once I/SigI is << 1 the data is no use.. Looking at those statistics I
would cut the resolution to 2.75.

What does the I2 data processing report suggest as the cut off?
Eleanor

On Fri, 30 Sept 2022 at 17:21, Andrew Purkiss <
a.purk...@mail.cryst.bbk.ac.uk> wrote:

> Is the data anisotropic? This would explain the strange processing
> statistics beyond 3.0 Angstrom. If using Dials directly it is worth
> looking for abnormalities with the reciprocal lattice viewer.
>
> I've seen similar issues with the completeness being low, when data is
> weak in one direction, despite reflections being reported in the
> scaling output.
>
> It may also be worth running some analysis of the data with Staraniso
> (https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi) to try to
> help.
>
> Andy
>
>
>
>
> Quoting Martin Malý :
>
> > Dear Matt,
> >
> > thank you for asking. I am bit confused how you set up the PAIREF
> > run. In paired refinement, data are added step by step - going to
> > higher resolution, i.e. lower d_hkl. So the merged data in the
> > PAIREF input should not be cut to much. The data statistics look
> > from DIALS quite strange, there is very good completeness and CC1/2
> > for high resolution shells, but very poor  and Rmeas.
> >
> > I would suggest to refine the model at 3 A to be safe. Then, run
> > PAIREF with the initial resolution 3 A and using the cutoffs 2.8,
> > 2.6, 2.4 and 2.2 A. Diffraction data must be up to 2.2 A in that
> > case, no truncation to 2.4 A as you mentioned previously.
> >
> > I hope it will help. Please feel free to ask and let me know if it
> > was successful.
> >
> > Best regards,
> > Martin
> >
> >
> > On 30. 09. 22 17:29, Matt McLeod wrote:
> >> Hi all,
> >>
> >> I am having a bit of trouble with PAIREF.  I am trying to determine
> >> the resolution cutoff of a dataset which has a high Rwork
> >> (0.223)/free (0.275)value for the resolution (2.24A).  I have
> >> truncated this data further to 2.4A and the R values get better but
> >> the electron density maps do not improve whatsoever.  When I put
> >> this data into PAIREF I get this message.
> >>
> >> WARNING: There are only 40 < 50 free reflections in the resolution
> >> shell 2.75-2.70 A. Values of statistics Rfree and CCfree in this
> >> shell could be misleading. Consider setting thicker resolution
> >> shells.
> >>
> >> This error occurs for all resolution bins.  Looking at the pdb log
> >> of the refined structure (where the data looks quite reasonable,
> >> maybe not a 2.3 dataset but not much worse).
> >>
> >> REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
> >> REMARK   3   BIN  RESOLUTION RANGE  COMPL.NWORK NFREE   RWORK
> >> RFREE  CCWORK CCFREE
> >> REMARK   3 1   60.08 -4.281.00 4135   213  0.1646
> >> 0.2213   0.940  0.901
> >> REMARK   3 24.28 -3.401.00 4095   201  0.1951
> >> 0.2672   0.928  0.857
> >> REMARK   3 33.40 -2.971.00 4099   204  0.2736
> >> 0.3303   0.861  0.739
> >> REMARK   3 42.97 -2.701.00 4026   212  0.3486
> >> 0.3508   0.726  0.551
> >> REMARK   3 52.70 -2.510.78 3178   154  0.4027
> >> 0.4062   0.637  0.594
> >> REMARK   3 62.50 -2.360.29 115460  0.4118
> >> 0.3984   0.647  0.547
> >> REMARK   3 72.36 -2.240.01   29 1  0.3366
> >> 0.4089   0.343  0.000
> >>
> >> Where I assume NFree is the issue, but doesn't suggest that there
> >> arent enough reflections.  There needs to be a higher cutoff as the
> >> completeness goes to pot, but the scaling log from DIALS suggested
> >> it was at least a good starting point.
> >>
> >>  Statistics by resolution bin:
> >>  d_max  d_min   #obs  #uniq   mult.  %comp   
> >> r_mrg   r_measr_pim   cc1/2   cc_ano
> >> 118.81   5.97  10436   15776.62  99.94 797.6
> >> 22.80.1100.1200.046   0.992*  -0.397
> >>   5.97   4.74   9602   15496.20 100.00 491.7
> >> 10.00.1720.1880.075   0.979*  -0.240
> >>   4.74   4.14  10410   15286.81 100.00 513.5
> >> 10.30.1910.2070.079   0.978*  -0.281
> >>   4.14   3.76  10833   15516.98 100.00 324.7
> >> 6.90.2380.2570.098   0.969*  -0.419
> >>   3.76   3.49  10956   15267.18 100.00 207.5
> >> 4.60.2590.2800.105   0.975*  -0.271
> >>   3.49   3.29  10899   15467.05 100.00 133.4
> >> 3.10.2720.2940.111   0.966*  -0.258
> >>   3.29   3.12   9565   15286.26  99.93  86.9
> >> 2.00.3140.3430.136   0.935*  -0.346
> >>   3.12   2.99   9256   1519

Re: [ccp4bb] suggestions on refinement of a protein-ligand complex

[Eleanor Dodson]

We probably need more detail to help you.
Have you looked carefully at the data processing? Is the Rmerge or Rpim
reasonable for all batches?   Is there any suggestion of twinning? Does the
wilson plot look linear? (These hexagonal SGs can be twinned)

How many copies of your molecule do you expect?  Then the model you have
used.. What is the sequence ID to the protein, and do you have a suitable
model for the ligand?
I would run a search in all possible SGS - and do the results clearly
indicate one choice is better than all others>

The final check is in the refinement - does the R value fall (FreeR should
too, but your resolution is rather low

Now you run the molecular replacement in all possible spacegroups for  that
pointgroup.. Is there a clear indication of one being preferred?
Good luck. Eleanor


On Tue, 13 Sept 2022 at 18:29, Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Dear Deepak,
>
> I guess that the spacegroup in the MTZ file that you use for refinement is
> wrong.
>
> I think you should carefully check the output of PHASER, and in particular
> the PDB file that it wrote. The correct spacegroup is given there (and it
> may also be P4122  or P4222 or P4322, because likely you used the PHASER
> option that tests all possibilities), and you will have to create a MTZ
> file for refinement that has that particular spacegroup in its header.
>
> Hope this helps, & best wishes
> Kay
>
> On Tue, 13 Sep 2022 11:20:44 +0200, Deepak Deepak 
> wrote:
>
> >Dear all,
> >
> >Greetings from Munich. I hope everything is well with you. I am writing to
> >take input on a problem related to the structure solution of a
> >protein-ligand complex.
> >
> >I have crystallized a protein (7.6kDa) with a ligand (5.2kDa). The crystal
> >diffracted to *2.71 Angstron*, and the data were processed using XDS.
> >During the XDS processing, Pointless suggested data be either P6222 (180
> >space group) or P6422 (181 space group) with a 98% probability.
> >The data were processed as *P6422*.
> >
> >Afterward, I ran Phaser MR with protein's PDB as a search ensemble, and I
> >found a good solution (with a good TFZ score) for protein alone, where I
> >could see some weak density for my ligand.
> >In the next step, I ran Phaser MR with a *modeled PDB* of the Ligand as
> >search ensemble + *using the partial solution from the previous Phaser MR
> >run of Protein*. This Phaser MR run gave me a good fit of ligand onto
> >protein surface with nice density for both molecules.
> >
> >Next, I went ahead with the refinement of this complex. The R-free, in the
> >beginning, was 0.55. In the first round of refinement, it went down to
> >*0.53,* but in the subsequent rounds, it even* increased*. I am stuck at
> >this point and unsure how to proceed. I tried different strategies to
> >refine it, but nothing worked.
> >Could the space group have been wrong? How can I make sure that? I can
> >provide a more detailed explanation to help you better understand the
> >problem.
> >I appreciate your suggestions and input on this matter.
> >
> >Kind regards,
> >Deepak,
> >Ph.D. student,
> >LMU Munich, Germany.
> >
> >
> >
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> 
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[ccp4bb]

[Eleanor Dodson]

Is that the right way round? Atomic no K 19,  Na 11

Call something K when it should be NA - B factor will shoot to reduce the
atom contribution.
Call something Na when it should be K - B factor will become very small..

As you say - check which fits best with the surrounding atoms..



On Thu, 8 Sept 2022 at 14:16, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello, K will always have a higher B-factor for a given piece of density
> due to it having a larger atomic number. Is the K B-factor much higher than
> those of neighbouring atoms and, if not, it's probably the best
> interpretation? Cheers, Jon.C.
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 8 Sep 2022, 14:07, smita yadav < sm...@rcb.res.in> wrote:
>
>
> Dear Community,
> Can you tell me. if we fit some metal in X-ray
> structure and its geometry and other properties are satisfied but showing
> some higher B-factor. does it validate to put that metal-ligand.ligand. At
> one site 2 metals such as K and NA fit, but K shows a higher B-factor, but
> other parameters such as geometry and other fit better for K instead of NA.
> So, out of the two ligands at the same site which one would be more
> favorable to be fit.
> --
>
> On Thu, Sep 8, 2022 at 6:35 PM smita yadav  wrote:
>
>>
>> Dear Community,
>> Can you tell me. if we fit some metal in X-ray
>> structure and its geometry and other properties are satisfied but showing
>> some higher B-factor. does it validate to put that metal-ligand.ligand. At
>> one site 2 metal such as K and NA fits, but K shows higher
>> --
>> Regards,
>> Smita Yadav
>> Ph.D SRF
>> Regional Centre for biotechnology,
>> Haryana-121001.
>>
>
>
> --
> Regards,
> Smita Yadav
> Ph.D SRF
> Regional Centre for biotechnology,
> Haryana-121001.
>
> --
>
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Re: [ccp4bb] Lower b-factors with increasing T

[Eleanor Dodson]

Hmmm - very puzzling..
One expects the  for the atoms to more or less match the Wilson B for
the data sets..

There are some mini bugs which can mislead you.
Is your average a mean or an RMS value? RMS ones can be hugely inflated if
you have a few crazily high Bs and the refinement programs can output
these. A misplaced LYS can give B factors >>200 - the software is trying to
tell you the atoms are not there - but the average B value calculations
don't know that!

Then if you have refined using TLS the "B factor" associated with each atom
is rather poorly defined. Is it a ad on the the vibration described by the
TLS or not?
And I am sure there are other aberrations I haven't thought of..

Then there is the issue of the initial scaling. Typically we scale all
batches to the first for a crystal believing that will be the most ordered..
If you scaled all data sets together you would expect them all then to have
more or less the same overall Wilson B.

Interesting challenges but the  values you quote are bizarre. I presume
all the models are the same?
Eleanor







On Thu, 8 Sept 2022 at 10:41, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Graeme
>
> good to know that I haven’t forgotten everything.
>
> Rgarding the data collection - I don’t think the OP mentioned how many
> crystals were used in the data collection (unless, of course, I’ve been
> reading even less carefully than normal…).
>
> Harry
>
> > On 8 Sep 2022, at 10:29, Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Hi Harry,
> >
> > You’re not wrong - “conventional wisdom” these days is pointing to CC of
> about 0.3 but I suspect that the difference is pretty modest in general
> >
> > However, in the case, the difference could have an impact as the higher
> resolution reflections may have something to say about the overall B factors
> >
> > I also wondered about the order of the data collection in this case,
> since there will probably be a certain amount of radiation damage across
> this number of data sets at non-cryo temperatures
> >
> > Best wishes Graeme
> >
> >> On 8 Sep 2022, at 10:21, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>
> >> hi folks
> >>
> >> I’ve been away from data processing for a while, but am I alone in
> thinking that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of
> useful data? I seem to remember that AutoProc and xia2.multiplex use a
> default of >= 0.3.
> >>
> >> Harry
> >>
> >>> On 7 Sep 2022, at 19:46, Matt McLeod  wrote:
> >>>
> >>> Hi everyone,
> >>>
> >>> I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A),
> 313K (2.2A) and I am curious as to the details in determining B-factors.
> >>>
> >>> I have treated these datasets more-or-less identically for
> comparison's sake.  I used DIALS to index, integrate, and scale the data.
> I scaled the data to a ~0.6 CC1/2 cutoff.
> >>>
> >>> After fully refining the datasets, there is an odd trend with respect
> to temperature (from what has been previously published) and I assume that
> this is because of "behind-the-scenes" computation rather than a
> biophysical observation.  The B-factors slightly decrease from 252-293K,
> and then significantly drop at 313K.  The maps look pretty well identical
> across the datasets.
> >>>
> >>> 253K - 53.8 A^2
> >>> 273K - 48.4 A^2
> >>> 293K - 45.5 A^2
> >>> 313K - 18.6 A^2
> >>>
> >>> I compared the wilson intensity plots from DIALS scaling for 273K and
> 313K and they are very comparable.
> >>>
> >>> I am looking for suggestions as to where to look at how these
> b-factors are selected or how to validate that these B-factor are or are
> not accurate.  Also, any relevant literature would be welcomed.  From what
> I have read, there is a general trend that as T increase, the atoms have
> more thermal energy which raises the b-factors and this trend is universal
> when comparing datasets from different temperatures.
> >>>
> >>> Thank you and happy to supply more information if that is helpful,
> >>> Matt
> >>>
> >>>
> 
> >>>
> >>> To unsubscribe from the CCP4BB list, click the following link:
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> >>>
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> >>
> >> 
> >>
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Re: [ccp4bb] Odd Positive Density Around a Cystine

[Eleanor Dodson]

The high peak is to be expected if the B factor is ludicrously too high.
I think the problem is in the behavior of the B factor refinement.
Try setting all B factors for the CYS to some sensible value (you can do
that in COOT - ) then see what happens after more cycles of refinement..

Eleanor



On Wed, 10 Aug 2022 at 17:09, Tristan Croll  wrote:

> I've seen this happen with B-factor refinement reasonably often. As I
> understand it the basic problem is that for small B-factors the gradient
> d(density)d(B) is large, but for large B-factors the gradient is small. So
> if the starting B-factor on an atom is very low and substantially lower
> than what the density supports, then the first refinement cycle can
> overstep to the point where there's almost no gradient, so future
> refinement steps don't pull it back down. Tightening the B-factor
> similarity restraints to surrounding atoms can help.
> --
> *From:* CCP4 bulletin board  on behalf of Thomas,
> Leonard M. 
> *Sent:* 10 August 2022 17:01
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* Re: [ccp4bb] Odd Positive Density Around a Cystine
>
> While the B value in the starting model was fine.  I did drop it to a
> reasonable value and it now seems to be behaving, was thinking about trying
> that before I posted.  Since this was an  MR determination I did check and
> the starting model B value was actually smaller then the surrounding
> residues.  I guess some thing went odd with the first round of refinement.
>
> Thank you for the suggestions.
>
> Len
>
>
> > On Aug 10, 2022, at 10:25 AM, Dale Tronrud 
> wrote:
> >
> >
> >   A large B value with positive difference density sure implies a
> convergence problem with the refinement.  Was the B value extreme in your
> starting model?  (A starting B that is wildly too large or too small at the
> start may cause it to become trapped in the refinement.) Maybe if you rerun
> your refinement with a moderate starting value for the B you will end up a
> more sensible result.
> >
> >   The only other way to end up with a parameter that directly conflicts
> with the difference density is a bad restraint, but that doesn't sound
> likely based on your description.
> >
> > Dale Tronrud
> >
> > On 8/10/2022 7:59 AM, Thomas, Leonard M. wrote:
> >> Hello All,
> >> I have run into something odd.  In working on a structure for one of
> the groups I work with regularly, on one of the cystine residues I have a
> very large positive density peak at the sulfur position. The B value is
> approximately 4 times the other values in the residue and on other cystine
> residues.  The overall structure has 2 molecules in the asymmetric unit
> and the corresponding cystine  on the other monomer is behaving as I would
> expect.   There are no disulfides in the structure.
> >> The data were collected on 9-2 at SSRL and all three of the data sets
> we collected show the same thing, all data go to about 2.2 angstroms.  We
> are trying to determine the ligand binding in the molecule but this cystine
> is not involved in ligand binding.  In house and other synchrotron data
> from previous protein preps and data collection runs of the same molecule
> grown in very similar condition and crystallized in the same space group
> have the residue behaving normally.
> >> I am open to any ideas as to what may be going on as I am rather
> puzzled by this.
> >> Thanks for any input,
> >> Len Thomas
> >> Leonard Thomas, Ph.D.
> >> Biomolecular Structure Core, Director
> >> Oklahoma COBRE in Structural Biology
> >> Price Family Foundation Institute of Structural Biology
> >> University of Oklahoma
> >> Department of Chemistry and Biochemistry
> >> 101 Stephenson Parkway
> >> Norman, OK 73019-5251
> >> Office: (405)325-1126
> >> lmtho...@ou.edu 
> >>
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ou.edu%2Fstructuralbiology%2Fcobre-core-facilities%2Fmcldata=05%7C01%7Ctic20%40universityofcambridgecloud.onmicrosoft.com%7C993e277f8ad542f6a9ae08da7ae9bba0%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637957441549582999%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=chxTRCdc%2FODmxM7NzVaZcAaXDJ0zMDulcWQrF%2FERs7A%3Dreserved=0
> <
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ou.edu%2Fstructuralbiology%2Fcobre-core-facilities%2Fmcldata=05%7C01%7Ctic20%40universityofcambridgecloud.onmicrosoft.com%7C993e277f8ad542f6a9ae08da7ae9bba0%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637957441549582999%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=chxTRCdc%2FODmxM7NzVaZcAaXDJ0zMDulcWQrF%2FERs7A%3Dreserved=0
> >
> >> 
> >> To unsubscribe from the CCP4BB list, click the following link:
> >>
> 

Re: [ccp4bb] Spam email after sending mail to ccp4bb

[Eleanor Dodson]

Is it spam? It is from a contributor to CCP4BB and I guess it says
something like - received your message - my Chinese rather rusty..
Eleanor

On Mon, 1 Aug 2022 at 18:26, Andrew Leslie - MRC LMB <
and...@mrc-lmb.cam.ac.uk> wrote:

> Every time I send an email to ccp4bb, I get a spam email from
> 295981...@qq.com that consists of a single line of Chinese (Japanese)
> characters, is anyone else getting this?
>
> Thanks,
>
> Andrew
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] AW: [ccp4bb] Regarding the correct space group identification

[Eleanor Dodson]

I cant see how the C2 cell can be reindexed to the P/mmm one?
Am I right to assume these are different processing of the same
diffraction?
And how many molecules do you have in each cell?
Eleanor



On Thu, 28 Jul 2022 at 12:52, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear Sayan,
>
>
>
> Thank you for this information. Why are your spots overlapping? The axes
> of your crystal are not particularly long. Did you put the detector very
> close to the crystal, or are there multiple diffraction patterns?
>
>
>
> Did you run Zanuda on your P1 structure? What Rfactors do you get when you
> complete the refinement in P1?
>
>
>
> Best regards,
>
> Herman
>
>
>
> *Von:* Sayan Saha 
> *Gesendet:* Donnerstag, 28. Juli 2022 11:43
> *An:* Schreuder, Herman /DE 
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] Regarding the correct space group identification
>
>
>
> Dear Sir,
>
>
>
> 1. There are no ice-rings. However, diffraction spots seem to be
> overlapping. This can be seen during the data processing, as the space
> group (C2 or P222) varies even in the consecutive frames.
>
>
>
> 2. Crystal packing of C2 and P22121 seem to be similar (please see the
> attached images).
>
>
>
> 3. Forgot to mention in my previous email that we have already processed
> the data in P1 and MR solution could be found only in P1 (Phaser was used
> with an option in all possible space groups of that point group).
>
>
>
> Please let me know if any other information is required.
>
>
>
> With best regards,
>
> Sayan Saha.
>
>
>
>
>
> On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
> Dear Sayan,
>
>
>
> If a subunit is correctly oriented, but the translation is incorrect,
> density for a ligand may still show up in the binding site of the protein.
> It might be that one of the 2-fold axes, you think is crystallographic, is
> in fact non crystallographic and a few Angstroms away from the
> crystallographic position.
>
>
>
> What I would do:
>
>1. Check the images: are there ice-rings or other artifacts that could
>cause scaling problems that would lead to high Rw/Rf values? In that case,
>there is not much you can do.
>2. Compare the C2 and P22121 solutions: do they have the same overall
>crystal packing (CS+NCS), or are they different? Do they have the same
>Rw/Rf values? Can we learn anything from the differences in overall crystal
>packing?
>3. Process, run MR and refine in P1. Do you get lower R-factors? If
>so, then run Zanuda to find out the real space group.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Sayan
> Saha
> *Gesendet:* Donnerstag, 28. Juli 2022 08:15
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] Regarding the correct space group identification
>
>
>
> Dear All,
>
>
>
> We have collected home-source X-ray intensity data for a protein at 2.6
> Angstrom. The data can be processed in either C2 (a=120, b=80, c=85 and
> beta=115) or P222 (P22121, a=80, b=85, c=110). MR solution can be obtained
> in both the space groups. However, the solution can be refined with an
> Rw/Rf of 29/32% only. The protein is bound to a ligand (co-crystallization)
> for which a clear density can be observed.
>
>
>
> Any help and suggestion in this regard would be very helpful.
>
>
>
> With best regards,
>
> Sayan Saha.
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> --
>
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>



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Re: [ccp4bb] Comparing two datasets

[Eleanor Dodson]

Indeed Jon you are right.
If you want to know whether to merge two dasta sets, use SCALEIT for
analysis..

If You actually want to merge the data. best to go back to each unmerged
and feed both into pointless/aimless etc, although you can cheat be letting
pointless square the given Fs then merge those two - not good practice but
possible..
Eleanor

On Tue, 26 Jul 2022 at 13:34, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello again, as far as I can tell, the question is about two already
> merged/unique datasets which Mirek wishes to merge into one. As far as I
> can tell/remember, Scaleit is for scaling datasets side-by-side to get
> isomorphous differences, etc, and I don't know of a way that you could get
> it to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit
> R-factors are different from R-merge, although the latter might be a bit
> dubious in the circumstances. Anyway, I think the Combat route is a viable
> way of achieving what the questioner wants to achieve ;-0
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com> wrote:
>
>
> Dear Colleagues,
> Scaleit is a terrific program.
> Amongst its strengths already listed I would also mention its breakdown
> table with F so that in the strongest F reflections bin any systematic
> errors between the two data sets can show up if the Rfactor is greater than
> about 1%.
> Greetings,
> John
> Emeritus Professor John R Helliwell DSc
>
>
>
>
> On 26 Jul 2022, at 11:40, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> 
> Not only does SCALEIT do the job - it presented useful plots and an
> informative log file..
> Eleanor
> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously
> the columns from each Xtal will need different labels..)
>
> On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:
>
>> If you give Pointless Fs, it squares them to Is (not correct if the Fs
>> have been derived from the truncate procedure, but not too bad). It will
>> then give you a comparison. If you give the two datasets to Pointless,
>> labelling them as different datasets, you can use Aimless to compare them
>>
>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but
>> still works and gives lots of statistics
>>
>> Phil
>>
>> Sent from my iPhone
>>
>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB <
>> and...@mrc-lmb.cam.ac.uk> wrote:
>>
>> I think that POINTLESS works with intensities rather than structure
>> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much
>> more detailed breakdown (R factors as a function of resolution and
>> differences in terms of sigmas etc) than POINTLESS WILL.
>>
>> Cheers,
>>
>> Andrew
>>
>> On 26 Jul 2022, at 09:24, LEGRAND Pierre <
>> pierre.legr...@synchrotron-soleil.fr> wrote:
>>
>> Hello Mirek,
>>
>> A very quick approach for that is offered by pointless:
>>
>> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
>> or
>> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>>
>> You will obtain a table looking like that, taking into account to
>> possible reindexing:
>>
>> Alternative indexing scores relative to reference
>>Alternative reindexingLklhd  CC R(E^2)Number
>> Cell_deviation
>>  1  [h,k,l]  0.9930.9620.118
>> 19150  0.08
>>  2  [-k,h,l] 0.0070.0780.512
>> 19150  0.87
>>
>>
>> Best wishes,
>>
>> Pierre Legrand
>> PROXIMA-1 Beamline
>> Synchrotron SOLEIL
>>
>> --
>> *De: *"Nicolas Foos" 
>> *À: *CCP4BB@JISCMAIL.AC.UK
>> *Envoyé: *Mardi 26 Juillet 2022 08:36:35
>> *Objet: *Re: [ccp4bb] Comparing two datasets
>>
>> Hi Mirek,
>>
>> I am pretty sure XSCALE will do that for you :
>> https://xds.mr.mpg.de/html_doc/xscale_program.html
>>
>> If not, maybe have a look on SHELXC in SIR mode.
>>
>> Hope this help.
>>
>> Nicolas
>> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>>
>> Hi,
>> I would like to calculate the R-merge for Fs from two datasets processed
>> from two different crystals. Tried to use Blend but got the message that
>> Blend requires R. Downloaded R but do not know how to tell CCP4 where it is
>> located on my Mac. Is there another program that would take two mtg

Re: [ccp4bb] Comparing two datasets

[Eleanor Dodson]

Not only does SCALEIT do the job - it presented useful plots and an
informative log file..
Eleanor
(You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and obviously the
columns from each Xtal will need different labels..)

On Tue, 26 Jul 2022 at 09:45, Phil Evans  wrote:

> If you give Pointless Fs, it squares them to Is (not correct if the Fs
> have been derived from the truncate procedure, but not too bad). It will
> then give you a comparison. If you give the two datasets to Pointless,
> labelling them as different datasets, you can use Aimless to compare them
>
> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but
> still works and gives lots of statistics
>
> Phil
>
> Sent from my iPhone
>
> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB <
> and...@mrc-lmb.cam.ac.uk> wrote:
>
> I think that POINTLESS works with intensities rather than structure
> factors (I’m not sure if this can be changed). Also, SCALEIT gives a much
> more detailed breakdown (R factors as a function of resolution and
> differences in terms of sigmas etc) than POINTLESS WILL.
>
> Cheers,
>
> Andrew
>
> On 26 Jul 2022, at 09:24, LEGRAND Pierre <
> pierre.legr...@synchrotron-soleil.fr> wrote:
>
> Hello Mirek,
>
> A very quick approach for that is offered by pointless:
>
> pointless HKLREF 1_1_aimless.mtz  HKLIN 2_1_aimless.mtz
> or
> pointless HKLREF 1_1_aimless.mtz  XDSIN XDS_ASCII.HK
>
> You will obtain a table looking like that, taking into account to possible
> reindexing:
>
> Alternative indexing scores relative to reference
>Alternative reindexingLklhd  CC R(E^2)Number
> Cell_deviation
>  1  [h,k,l]  0.9930.9620.118
> 19150  0.08
>  2  [-k,h,l] 0.0070.0780.512
> 19150  0.87
>
>
> Best wishes,
>
> Pierre Legrand
> PROXIMA-1 Beamline
> Synchrotron SOLEIL
>
> --
> *De: *"Nicolas Foos" 
> *À: *CCP4BB@JISCMAIL.AC.UK
> *Envoyé: *Mardi 26 Juillet 2022 08:36:35
> *Objet: *Re: [ccp4bb] Comparing two datasets
>
> Hi Mirek,
>
> I am pretty sure XSCALE will do that for you :
> https://xds.mr.mpg.de/html_doc/xscale_program.html
>
> If not, maybe have a look on SHELXC in SIR mode.
>
> Hope this help.
>
> Nicolas
> On 25/07/2022 21:52, Cygler, Miroslaw wrote:
>
> Hi,
> I would like to calculate the R-merge for Fs from two datasets processed
> from two different crystals. Tried to use Blend but got the message that
> Blend requires R. Downloaded R but do not know how to tell CCP4 where it is
> located on my Mac. Is there another program that would take two mtg files
> and merge the Fs?
> Any help would be greatly appreciated.
> Mirek
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
> Nicolas Foos PhD - ARISE fellowhttps://orcid.org/-0003-2331-8399
>
> EMBL Grenoble, McCarthy Team
> 71 av. des Martyrs,
> 38000 Grenoble FRANCE
>
> +33 4 57 42 84 67
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
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>
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>
>
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Re: [ccp4bb] symmetry possibilities

[Eleanor Dodson]

eleanorOh dear - why don’t crystals behave better!

Re twinning - do the data processing Plots indicate twinning?  ( L test?2nd
moments?)

It sounds rather more like overlapping diffraction where only some of the
observations are Affected.

Eleanor

On Thu, 21 Jul 2022 at 10:50, Flaig, Ralf (DLSLtd,RAL,LSCI) <
8308ad6ea74c-dmarc-requ...@jiscmail.ac.uk> wrote:

> This paper by Pietro Roversi might help:
>
> https://journals.iucr.org/d/issues/2012/04/00/ba5182/index.html
>
>
> Kind regards,
> Ralf
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kay
> Diederichs
> Sent: 20 July 2022 22:11
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] symmetry possibilities
>
> Dear Jorge,
>
> what you write makes sense to me, and I cannot answer your questions. This
> is just to say that the situation you encounter is not completely uncommon,
> although most crystallographers would abandon such a crystal form, I guess.
> The technical term that describes this 4-fold twinning is "tetartohedral
> twinning" (in contrast to merohedral twinning, which involves two twin
> domains); maybe this helps to find additional pointers.
>
> best wishes,
> Kay
>
> On Wed, 20 Jul 2022 11:10:04 -0300, Jorge Iulek  wrote:
>
> >Dear all,
> >
> >
> >  We had some data collections at a Synchrotron. Crystals are a
> >kind of brush like (lattice strains, to use a term by Dr. Bergfors,
> >though we employed good effort for purification), but we took advantage
> >of the Synchrotron microfocus.
> >
> > Some of the datasets (images) clearly shows more than one lattice
> >(maybe more than two) that, struggling, we managed to process a get a
> >dataset which allowed molecular replacement and then (initial) refinement.
> >
> > But, in a second Synchrotron travel (and after efforts for
> >improving crystals), we got in some cases images with spots "well
> >separated'  "unique lattice" at some of the target spots (radiation on
> >the crystal) in the crystal.
> >
> > We processed these happily to P212121 (though some strange points
> >by pointless and/or xtriage, namely that " the L-test suggests that the
> >data may be twinned,  so the indicated Laue symmetry may be too high").
> >Systematic absences seem to be OK for lower resolution reflections, but
> >at higher resolution there seems to be more of a modulation (if a look
> >at a P222 processing).
> >
> > Anyway, we took, initially, refinement at P212121, nevertheless (I
> >should say not surprisingly), it stuck at 30/31 % R-free, model close
> >(if not at all) to completion. Data resolution is 2.31 A.
> >
> > We went to process these images in P1, and in the three possible
> >P21  (named P21_45, P21_122 and P21_155 - according to approx. axis
> >dimensions) sg's. Then we went to refine (refmac, twin option) the
> >current model (and then due "symmetry copies" produced with pdbset and
> >added to the model to be refined,) in all possible space groups, and
> >*care was taken* to  inherit the former r-free set *and* make the then
> >corresponding twin related reflections to be in the r-free set (to be
> >close to 5% of reflections, but "independent" reflections). It turned
> >out that the R/Rfree values dropped around to ~19/25% for P1 and one
> >(namely, P21_b151) of the P21; higher values for other P21's. As
> >expected, twin domains refine more or less close to 25 (P1) and 50%
> >(any P21), respectively.
> >
> > To mess up a bit more, I made the same study with "another dataset"
> >(another illuminated spot on the - same - crystal). In this case, only
> >the dataset processed in P1 presented "good" R values.
> >
> > I think these observations might correlate to what the "crystal "
> >physically is... a mix of portions genuinely P212121 but mixed, more or
> >less, that in some places with twins in one or more other types,
> >depending on where I focus my beam.
> >
> > Should I look at anything else to establish twin P1 is the best
> >way to refine this structure?
> >
> >
> > Related, and a question I mentioned before in this forum: what if
> >a genuine 2 axis (say , P222 to P2, or even to P1) (I do not mean this
> >is the case here) is ignored such that one would have doubled the
> >number of observations but also doubled the number of parameters to be
> >refined (suppose to exclude NCS in any case). Would one expect R/Rfree
> >values to be similar in both P222 and P2 (or even P1)? How much extra
> >freedom would one have besides the twin domain fractions to refine?
> >
> >
> > Yours,
> >
> >
> >Jorge
> >
> >###
> >#
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> >mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> >available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> 

Re: [ccp4bb] Determining space group

[Eleanor Dodson]

Yes - I wondered how much data can be extracted from each crystal..
Eleanor

On Fri, 22 Jul 2022 at 19:23, Kay Diederichs 
wrote:

> Hi Eleanor,
>
> yes, for sufficiently complete datasets a reference dataset is enough.
> But in serial crystallography, there is typically little overlap between
> individual data sets. And the data quality is often low.
>
> In my posting I forgot to say that CrystFEL also has a facility to
> overcome indexing ambiguity.
>
> Best wishes,
> Kay
>
> On Fri, 22 Jul 2022 19:02:19 +0100, Eleanor Dodson <
> eleanor.dod...@york.ac.uk> wrote:
>
> >Surely once you have indexed one crystal, you can use the facility to
> check
> >the next ones indexing against the reference - aka pointless?
> >
> >On Fri, 22 Jul 2022 at 16:20, Kay Diederichs <
> kay.diederi...@uni-konstanz.de>
> >wrote:
> >
> >> Hi Monika,
> >>
> >> in June we had a summer school at MaxIV, and one of the topics was
> serial
> >> crystallography - with lectures and tutorials. Maybe you can talk to the
> >> people who attended the course, and the organizers, Ana Gonzalez and
> Thomas
> >> Ursby, and ask them for help.
> >>
> >> It is more difficult to determine the spacegroup in serial
> >> crystallography, compared to conventional crystallography. This is
> because
> >> there are several spacegroups that have an indexing ambiguity
> >> (non-equivalent ways to index a given diffraction pattern), e.g. P3, P4,
> >> P6, P321, ..., altogether 38 out of the 65 Sohncke groups . So just
> merging
> >> the data blindly may give you "computationally twinned" data. Take a
> look
> >> at doi:10.1107/S1399004713025431 .
> >>
> >> If you use XDS/XSCALE, you can analyze the scaled but unmerged data with
> >> xscale_isocluster .
> >> If you use DIALS, you could use dials.cosym for this purpose.
> >>
> >> Best wishes,
> >> Kay
> >>
> >> On Fri, 22 Jul 2022 09:51:14 +, Monika Bjelcic <
> >> monika.bjel...@maxiv.lu.se> wrote:
> >>
> >> >Hi,
> >> >
> >> >I’m hoping someone can help me how to determine a space group from my
> >> collection.
> >> >I did serial crystallography on a crystal that doesn’t have a cryo
> >> structure. I was able to determine the Point group but for the next step
> >> I’m stuck.
> >> >
> >> >Kind regards,
> >> >Monika Bjelcic
> >> >PhD student at BioMAX
> >> >[cid:image001.jpg@01D3B796.B7E175A0]
> >> >MAX IV Laboratory
> >> >Lund University
> >> >Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
> >> >Visiting address: Fotongatan 2, 224 84 Lund, Sweden
> >> >Mobile:  +46-761357994
> >> >
> >> >
> >>
> >
> >> >
> >> >To unsubscribe from the CCP4BB list, click the following link:
> >> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >> >
> >> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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> >> 
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Re: [ccp4bb] Determining space group

[Eleanor Dodson]

Surely once you have indexed one crystal, you can use the facility to check
the next ones indexing against the reference - aka pointless?

On Fri, 22 Jul 2022 at 16:20, Kay Diederichs 
wrote:

> Hi Monika,
>
> in June we had a summer school at MaxIV, and one of the topics was serial
> crystallography - with lectures and tutorials. Maybe you can talk to the
> people who attended the course, and the organizers, Ana Gonzalez and Thomas
> Ursby, and ask them for help.
>
> It is more difficult to determine the spacegroup in serial
> crystallography, compared to conventional crystallography. This is because
> there are several spacegroups that have an indexing ambiguity
> (non-equivalent ways to index a given diffraction pattern), e.g. P3, P4,
> P6, P321, ..., altogether 38 out of the 65 Sohncke groups . So just merging
> the data blindly may give you "computationally twinned" data. Take a look
> at doi:10.1107/S1399004713025431 .
>
> If you use XDS/XSCALE, you can analyze the scaled but unmerged data with
> xscale_isocluster .
> If you use DIALS, you could use dials.cosym for this purpose.
>
> Best wishes,
> Kay
>
> On Fri, 22 Jul 2022 09:51:14 +, Monika Bjelcic <
> monika.bjel...@maxiv.lu.se> wrote:
>
> >Hi,
> >
> >I’m hoping someone can help me how to determine a space group from my
> collection.
> >I did serial crystallography on a crystal that doesn’t have a cryo
> structure. I was able to determine the Point group but for the next step
> I’m stuck.
> >
> >Kind regards,
> >Monika Bjelcic
> >PhD student at BioMAX
> >[cid:image001.jpg@01D3B796.B7E175A0]
> >MAX IV Laboratory
> >Lund University
> >Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
> >Visiting address: Fotongatan 2, 224 84 Lund, Sweden
> >Mobile:  +46-761357994
> >
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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Re: [ccp4bb] AW: Determining space group

[Eleanor Dodson]

Most molecular replacement programs allow you to search in all possible
space groups consistent with a given point group.
Eleanor

On Fri, 22 Jul 2022 at 11:18, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Hi Monika,
>
>
>
> I would process the data using the point group information ignoring any
> possible screw axes, e.g. in space group P222, where the true space group
> might be P212121.
>
>
>
> The next step depends on how you plan to solve the structure. You mention
> that there is no cryo structure, do you mean cryoEM structure, or that you
> cannot freeze the crystals? If there is any search model available
> (crystal, cryoEM, alphaFold), I would run molecular replacement, using all
> possible space groups for your point group. This should resolve the correct
> space group.
>
>
>
> Good luck!
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Monika
> Bjelcic
> *Gesendet:* Freitag, 22. Juli 2022 11:51
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] Determining space group
>
>
>
> Hi,
>
>
>
> I’m hoping someone can help me how to determine a space group from my
> collection.
>
> I did serial crystallography on a crystal that doesn’t have a cryo
> structure. I was able to determine the Point group but for the next step
> I’m stuck.
>
>
>
> Kind regards*,*
>
> *Monika Bjelcic*
>
> PhD student at BioMAX
>
> *MAX IV Laboratory*
>
> Lund University
>
> Postal address: P.O. Box 118, SE-221 00 Lund, Sweden
>
> Visiting address: Fotongatan 2, 224 84 Lund, Sweden
>
> Mobile:  +46-761357994
>
>
>
>
> --
>
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> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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Re: [ccp4bb] Strange crystal packing in twined crystal

[Eleanor Dodson]

Hmmm - is there a smaller lattice which might fit the density? As Andrew
says there are examples of pseudo emptiness in crystals but there are more
examples of wrong lattices!
Check for non-crystallographic translation?
You could attach the pointless/aimless/etc log files..
Eleanor

On Fri, 22 Jul 2022 at 10:15, Andrew Leslie - MRC LMB <
and...@mrc-lmb.cam.ac.uk> wrote:

> Dear Florian,
>
>  There have been previous examples where there are
> distinct “layers” of protein packing without any obvious density linking
> the layers, as it appears in the image you show. One is tyrosyl tRNA
> synthetase, where the layers were in fact linked by a disordered domain for
> which there was no density. Does the density that you see account for the
> entire protein (or complex) that you have crystallised?
>
> I am fairly sure that this has also been seen for membrane proteins, where
> the extra-membrane component (or an additional protein, eg a Fab) has been
> disordered, again giving layers of density that appear unconnected.
>
> I’m not sure what you mean by “having two distinct lattices”. Do the
> diffraction images show any signs of disorder, eg diffuse streaking or
> features that are not accounted for by the lattice used when integrating
> the data?
>
> Best wishes,
>
> Andrew
>
> On 21 Jul 2022, at 19:29, Schubot, Florian  wrote:
>
> Hi, I have a high-resolution data set ~1.6 Angst.) for a twinned crystal
> (SG C2, twin law h,-k,-l). The structure was solved via molecular
> replacement. The map and model look excellent but R and Rfree continue to
> hover around 30%. I do use twinned refinement. Reviewing the packing, I
> noticed a huge gap between layers (picture below). There is NO additional
> well-defined protein density in this gap. I this gap is a symptom of having
> two distinct lattices. I was curious if anyone could advise/comment.
> Thank you,
> Florian
>
> 
>
> =
> Florian Schubot, Ph.D.
>
> Associate Professor
> Virginia Polytechnic Institute and State University
> Department of Biological Sciences
> 5002 Derring Hall
> 926 West Campus Dr
> Blacksburg, VA 24061
> United States
> E-mail: fschu...@vt.edu
> Phone: (540) 231-2393
> Fax: (540) 231.4043
> http://www.faculty.biol.vt.edu/schubot/
> =
>
> --
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Re: [ccp4bb] find clashes

[Eleanor Dodson]

Sorry to go back in time but distang is useful.
You set radii
Example:

 distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb

RADI CA 1

end

will give all CA withion 2A of each other

 distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb

end

Will give all C N O S within VDW contact. -


On Thu, 14 Jul 2022 at 17:28, Kay Diederichs 
wrote:

> Hi Henrike,
>
> I use CCP4's "contact" program:
>
> #!/bin/bash
> # find bad contacts: list all CA-CA distances < 3.8A between non-adjacent
> residues
> # in a well-folded protein, these should be very rare (1 contact in 1000
> residues)
> # KD 20.12.21
> grep CA $1 > /tmp/temp.pdb
> contact xyzin /tmp/temp.pdb < COLOR/{print}' | grep -v FONT
> MODE IRES
> LIMIT 0 3.8
> EOF
> rm /tmp/temp.pdb
>
> If you are interested in non-CA atoms, modify accordingly. But this should
> give you the idea.
>
> HTH,
> Kay
>
>
> On Thu, 14 Jul 2022 17:52:40 +0200, Henrike Wagler <
> henrike.wag...@studium.uni-hamburg.de> wrote:
>
> >Dear all,
> >
> >
> >We are looking into a way to find clashes / bumps between protein chains
> >(closer than van der Waals contacts).
> >
> >Ideally, we would like to that with a script, for example, reading in a
> >pdb file, and giving back the number of clashes.
> >Of course, this is possible within Coot or PyMol, but maybe there is a
> >software as part of CCP4 that we can directly use with a script.
> >
> >Apologies if there an obvious solution that we are currently not aware of.
> >
> >Many thanks
> >
> >Best,
> >Henrike Wagler
> >
> >
> >
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Re: [ccp4bb] Unidentified electron density

[Eleanor Dodson]

Did you check anomalous difference peaks? They would show zn very clearly.

On Sat, 2 Jul 2022 at 08:08, Sayan Saha  wrote:

> Dear all,
> As suggested by most people, we modeled   Zn2+   ions coordinated with
> three water molecules.
> Thanks for everyone’s response.
>
> With best regards,
> Sayan Saha
>
> On Fri, Jul 1, 2022 at 8:04 PM Jon Cooper 
> wrote:
>
>> Hello, I wonder if it is disorder i.e. alternative conformations of the
>> Asp and flexible Lys.
>>
>> Do let us know your final interpretation as we don't often, or indeed
>> ever, hear the final outcome of these mystery density competitions and I
>> would love to learn more from them.
>>
>> Cheers, Jon.C.
>>
>>
>> Sent from ProtonMail mobile
>>
>>
>>
>>  Original Message 
>> On 30 Jun 2022, 08:03, Sayan Saha < ssaha43...@gmail.com> wrote:
>>
>>
>> Dear All,
>>
>> I am trying to refine a protein structure. I observed an additional
>> electron density (Figures attached) connected to the aspartate residue.
>>
>> Any suggestion in this regard would be appreciated.
>>
>> With best regards,
>> Sayan Saha.
>>
>> --
>>
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Re: [ccp4bb] sequence search

[Eleanor Dodson]

Thank you Sameer.
I now know -
click th
Advanced Search link
in the RH top corner just below the Search box..
 Eleanor

On Fri, 24 Jun 2022 at 15:46, Sameer Velankar  wrote:

> Following seems to work for me -
>
>
> https://www.ebi.ac.uk/pdbe/entry/search/index/?searchParams=%7B%22q_fasta_sequence%22:%5B%7B%22value%22:%22PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE%22,%22condition1%22:%22AND%22,%22condition2%22:%22Contains%22%7D%5D,%22resultState%22:%7B%22tabIndex%22:0,%22paginationIndex%22:1,%22perPage%22:%22100%22,%22sortBy%22:%22fasta(e_value)%20asc%22%7D%7D
> <https://www.ebi.ac.uk/pdbe/entry/search/index/?searchParams=%7B%22q_fasta_sequence%22:[%7B%22value%22:%22PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE%22,%22condition1%22:%22AND%22,%22condition2%22:%22Contains%22%7D],%22resultState%22:%7B%22tabIndex%22:0,%22paginationIndex%22:1,%22perPage%22:%22100%22,%22sortBy%22:%22fasta(e_value)%20asc%22%7D%7D>
>
> If you replace the sequence “
> PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE
> <https://www.ebi.ac.uk/pdbe/entry/search/index/?searchParams=%7B%22q_fasta_sequence%22:[%7B%22value%22:%22PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE%22,%22condition1%22:%22AND%22,%22condition2%22:%22Contains%22%7D],%22resultState%22:%7B%22tabIndex%22:0,%22paginationIndex%22:1,%22perPage%22:%22100%22,%22sortBy%22:%22fasta(e_value)%20asc%22%7D%7D>”
> to what you have it should work. Be careful about the url characters either
> side of the sequence.
>
> Sameer
>
> On 24 Jun 2022, at 15:41, Eleanor Dodson 
> wrote:
>
> PDBe server - my long term favorite website...
>
> On Fri, 24 Jun 2022 at 15:40, Sameer Velankar  wrote:
>
>> Hi Eleanor
>>   I assume you are using PDBe service since you mention SSM or is this
>> from CCP4 interface?
>> Sameer
>>
>> On 24 Jun 2022, at 15:36, Eleanor Dodson <
>> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> The pdb seems to have gone so up market I can no longer see how to submit
>> a simple sequence search or rum SSM
>>
>> I get offered multiple options to use services I do not want to use!
>> But asking for
>> "sequence search" or Search sequences" gives lots and lots of
>> non-intuitive choices!
>> Grrr
>> Eleanor
>>
>> Any advice?
>>
>> --
>>
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>>
>>
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