Re: [ccp4bb] Rescale merged data?

[Robbie Joosten]

If I may add to that: Please deposit the full dataset, not just the set of reflections you end up using. This allows people to use all the data if they are interested.Cheers,RobbieOn 17 Apr 2024 22:35, "Hekstra, Doeke Romke"  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  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,



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On 17 Apr 2024 22:35, "Hekstra, Doeke Romke"  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 

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

[Robbie Joosten]

Make sure everything is built. Sometimes it is the crystallisation agents that 
sit at surprising places: 
https://onlinelibrary.wiley.com/doi/full/10.1002/pro.2923

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of
> Murpholino Peligro
> Sent: Tuesday, April 9, 2024 03:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] How to compare the same protein crystallized in different
> conditions?
> 
> 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




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Re: [ccp4bb] isymop reference for ISYM column in MTZ files

[Robbie Joosten]

If I understand the documentation correctly (https://www.ccp4.ac.uk/html/mtzformat.html), it refers to the symmetry operations as they are stored in the header of the MTZ file. So the source of the MTZ file might make a difference. The safest way of using this data is to follow the header and not some implied order.HTH,RobbieOn 15 Mar 2024 04:59, "Hekstra, Doeke Romke"  wrote:

Hi, 
 
I would like to be sure about which symmetry operation the M/ISYM column in an MTZ file is referring to. Is it correct that this matches the order in CCP4’s /lib/data/syminfo.lib (at least when this order is unique—it is not always so)?
 Would anyone know why the order in one of my favorite websites (http://img.chem.ucl.ac.uk/sgp/large/sgp.htm) happens to often be different?
 
Thank you,
Doeke
 
=  
 
Doeke Hekstra
Assistant Professor of Molecular & Cellular Biology, and of Applied Physics (SEAS),
Director of Undergraduate Studies, Chemical and Physical Biology
Center for Systems Biology, Harvard University
52 Oxford Street, NW311
Cambridge, MA 02138
Office:    617-496-4740
Admin:   617-495-5651 (Lin Song)
 
 




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Re: [ccp4bb] what is isomorphous?

[Robbie Joosten]

Hi Carlos,

In a practical setting you don't have to be very purist. The memory with 
respect to the reflection data is lost if you refine to convergence. Now there 
was are recent discussion on refinement convergence and again you can be quite 
purist here. However, if you go through a few cycles of rebuilding and 
refinement until R and R-free are stable, you are in clear with respect to 
cheating.*

HTH,
Robbie

When working with ligands there a much more severe ways of cheating (oneself).

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Carlos
> Kikuti
> Sent: Thursday, February 8, 2024 00:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] what is isomorphous?
> 
> Hello!
> 
> I have to admit my maths is a bit lazy, but this discussion got me stitched 
> up,
> because of a point I believe has not been addressed: the Rfree flags. I've 
> been
> trained to import Rfree flags whenever the crystals have the same space group
> and similar cell dimensions to the search model for molecular replacement -
> this to avoid "cheating" the Rfree validation with reflections that the search
> model has already 'seen'. We often work with series of crystals of the same
> proteins with different ligands, which give groups of very similar unit 
> cells. So
> far my strategy has been to mirror the Rfree flags (using the -ref or -rfree
> keyword in Autoproc) whenever the biggest difference in one of the dimensions
> is 5% - number just out of my instinct, taking in account the Rmerge of ~0.1 
> or
> less in the good cases. Maximum resolutions are between 2.7 and 1.9
> angstroms. Now considering the fact that isomorphism depends on resolution,
> it makes me reconsider the 5% cut-off: this might be fine at the low 
> resolution,
> but what about the higher resolution shells? What would be the best way to
> proceed in these cases, then? Because the level of 'cheating' will also vary 
> with
> resolution...
> 
> Carlos
> 
> On Sun, Dec 31, 2023 at 5:21 PM James Holton   > wrote:
> 
> 
> 
>   Ahh yes. I still have the very helpful email I got from Dame Louise
> Johnson in 2010.  I don't think she would mind my quoting it here:
> 
> 
> 
>   Dear James
> 
>   I was sorry to miss you when you were at Diamond - I was in
> Germany.
> 
>   The story of the two forms of lysozyme crystals goes back to
> about 1964 when
>   it was found that the diffraction patterns from different 
> crystals
> could be
>   placed in one of two classes depending on their intensities.
> This discovery
>   was a big set back at the time and I can remember a lecture
> title being
>   changed from the 'The structure of lysozyme' to 'The structure
> of lysozyme
>   two steps forward and one step back'.  Thereafter the  crystals
> were
>   screened based on intensities of  the (11,11,l) rows to
> distinguish them
>   (e.g. 11,11,4 > 11,11,5 in one form and vice versa in another).
> Data were
>   collected only for those that fulfilled the Type II criteria. 
> (These
>   reflections were easy to measure on the linear diffractometer
> because
>   crystals were mounted to rotate about the diagonal axis). As I
> recall both
>   Type I and Type II could be found in the same crystallisation
> batch .
>   Although sometimes the external morphology allowed
> recognition this was not
>   infallible.
> 
>   The structure was based on Type II crystals. Later a graduate
> student Helen
>   Handoll examined Type I. The work, which was in the early days
> and before
>   refinement programmes, seemed to suggest that the
> differences lay in the
>   arrangement of water or chloride molecules (Lysozyme was
> crystallised from
>   NaCl). But the work was never written up.  Keith Wilson at one
> stage was
>   following this up as lysozyme was being used to test data
> collection
>   strategies but I do not know the outcome.
> 
>   An account of this is given in International Table Volume F
> (Rossmann and
>   Arnold edited 2001) p760.
> 
>   Tony North was much involved in sorting this out and if you
> wanted more info
>   he would be the person to contact.
> 
>   I hope this is helpful. Do let me know if you need more.
> 
>   Best wishes
> 
>   Louise
> 
>   Armed with this advice, I searched the PDB using what I call the
> "Johnson ratio" of F(11,11,4) / F(11,11,5) and found there was a continuous
> spectrum (pasted below). The extrema of this spectrum were 3aw6 and 3aw7
> (circled), which are not only from the same paper, but from the same crystal: 
> a
> dehydration study.  Despite a modest unit cell size change of 0.7%, the 
> R-factor
> between the Fobs of 

Re: [ccp4bb] Automated refinement convergence

[Robbie Joosten]

Hi Robert,

I see your point but extending the number of cycles to reach convergence has a 
big risk of going into infinite loops (which you point out). In the case of 
Refmac stopping early is not really needed as it is very fast anyway; a few 
unnecessary cycles won't take that long. Generally it is better to err in the 
direction of having too many cycles than too few, especially in your 'final' 
refinement. This is also the logic applied to pdb-redo, it does 20 cycles by 
default (more than the typical number for Refmac) and then extends the number 
of cycles when it uses options that slow down convergence (jelly body, 
anisotropic B-factors, new data from paired refinement). This (almost) always 
leads to something that we can call "convergence", at least for models that 
were at the final stages of model building.

That said, I have only really achieved convergence in Refmac (i.e. gradients 
are '0') once in twenty years and that was after more than 500 cycles of jelly 
body refinement.* Apparently, there is a large step between "things don't 
change a lot anymore" and real convergence.   

Cheers,
Robbie

* Refmac crashed at that point. A division by zero if I remembered correctly.

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Robert
> Oeffner
> Sent: Thursday, January 18, 2024 12:05
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Automated refinement convergence
> 
> Hi,
> 
> I am wondering if authors of refinement programs would like to consider
> putting on their users wish list the ability of refinement programs to
> automatically terminate once the refinement has reached convergence. Various
> refinement metrics such as R factors, CC or RMS values typically will reach a
> plateau once the refinement of a macromolecular structure with X-ray or EM-
> data has converged and further macro-cycles of refinement will no longer
> improve the structure. The default number of macro-cycles in programs such as
> Phenix-refine and Refmac are probably sensible for most cases but in some
> cases it would be nice if the programs automatically extended the number of
> macro-cycles as needed (or decreased the number).
> 
> The user can of course examine log files from refinement themselves and
> decide whether to continue refinement. But since starting a new session of
> refinement appears to always create an initial fluctuation in the refinement
> metrics before they align with the values of the last macro-cycles in the
> previous refinement session, the user is compelled to do at least, say 3 or 
> more
> macrocycles in addition to whatever may be needed for reaching convergence. I
> guess it would therefore be more efficient if this was implemented directly in
> the refinement programs and presented as an option for the user to choose.
> 
> There could be cases where alternate conformations of a structure will
> repeatedly be oscillating in and out of density thus causing the refinement
> metrics also to oscillate. Hopefully such cases could be covered by gauging 
> the
> level of fluctuations of the refinement metrics and terminate the refinement
> accordingly.
> 
> Many thanks,
> 
> Robert
> 
> ###
> #
> 
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> 
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Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Robbie Joosten]

Hi Tom,I think restraints do change the data/parameter ratio, but how much is not straightforward. In, at least, the context of the Hamilton test restraints change the degrees of freedom which translates into a change of the effective data/parameter ratio. It is treated as adding extra observations albeit with some unknown weight. Ethan Merritt's way of handeling this unknown weight (which we implemented in bselect) is setting an upper limit for the weight and thus bracketing the value. Lets assume we have glycol. Adding individual B-factors instead of one overall B adds 3 extra parameters. We also add B-factor restraints: 3 bonded atom 1-2 restraints plus 2 angled atoms 1-3 restraints (in Refmac's implementation). So 3 extra parameters, 5 extra restraints. These restraints can at best nullify the effect of the extra parameters so their effective weight is maximum 3/5, but probably less. The weight of the restraints must be somewhere between 0 (e.g when the B-factor restraint weight in Refmac is set to zero) and 0.6 (the restraint weight is huge). Assuming that the restraints do something, the degrees of freedom go up with less than 3 for our glycol refinement. How much less is related to the restraint weight we set in Refinement. Cheers,RobbieOn 6 Jan 2024 23:26, Tom Peat  wrote:




Hello Robbie, 




Thanks for the stats and description of what has been done. 

I think this puts us back into the realm of restraints versus constraints and what is possible when trying to reduce the number of parameters to be refined. Although grouped B-factors don't capture the reality of side chains being more mobile, it is a constraint
 that reduces the number of parameters being refined and helps highlight regions of the structure which are more mobile (which a flat or average B-factor would not do). 

Making tighter restraints on the system as a whole doesn't change the data/parameter ratio, which can lead to its own issues, but is certainly better than just letting things go wild. 

As is often the outcome, we state 'it depends on your individual situation' and generally suggest looking at various possibilities until one finds some compromise which works. Not as intellectually gratifying as having a cut and dry answer to these questions
 that come up rather frequently. 

Thanks again for the stats and description. 

cheers, tom 




From: Robbie Joosten 
Sent: Sunday, January 7, 2024 8:24 AM
To: Tom Peat ; CCP4BB@JISCMAIL.AC.UK 
Subject: RE: [ccp4bb] Can Refmac5 refine temperature factor residue by group?
 


[You don't often get email from robbie_joos...@hotmail.com. Learn why this is important at

https://aka.ms/LearnAboutSenderIdentification ]

Hi Tom,

At 3A the median number of reflections per atom is 3.4 which is indeed lower than 4. So in unrestrained refinement the data/parameter ratio is indeed worse than 1. This is where the effect of the restraints really matter and starting from a flat B-factor model
 is interesting. This is what pdb-redo does if there are fewer than 4 reflections per atom. In such cases first TLS model are refined, one-group-per-chain (yes, that has room for improvement) plus any user-provided grouping. The TLS model that performs best
 in refinement is then kept (or no TLS model at all if they don't work). Given this TLS model, the structure model is refined with isotropic B-factors and flat B-factors. Both refinement results are then tested by a program called "bselect" that performs the
 Hamilton test plus some fallback test. The "best" model is then chosen. If this involves isotropic B-factors, the B-factor restraint weight is then optimised.

Some stats:
Of the 1958 cases in the databank, 573 are refined with a flat B-factor model (2.9 reflections/atom on average), 520 with isotropic B-factors and tighter-than-default restraint weights (3.8 reflections/atom on average), 612 with isotropic B-factors and looser-than-default
 weights (4.1 reflections/atom on average), the rest is isotropic with default weights (3.8 ref/atom).

So there is a trend given the number of reflections per atom but it is not that strong for individual cases. Testing is needed. I won't claim that this is the best protocol for each of the cases, but I guess they are decent starting points for most.

Cheers,
Robbie

> -Original Message-
> From: Tom Peat 
> Sent: Saturday, January 6, 2024 21:42
> To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten
> 
> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
>
> It appears that Zhonghao might be worried about his data to parameter ratio.
> At 3 A, one can easily be in a situation where one has fewer reflections than
> four times the number of atoms (X, Y, Z plus B).
> I like the idea of starting out with the average B (or even Wilson B) and then
> doing TLS as that should reduce the number of parameters being refined.
> Best regards, tom
>
> ____________

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

[Robbie Joosten]

Hi Tom,

At 3A the median number of reflections per atom is 3.4 which is indeed lower 
than 4. So in unrestrained refinement the data/parameter ratio is indeed worse 
than 1. This is where the effect of the restraints really matter and starting 
from a flat B-factor model is interesting. This is what pdb-redo does if there 
are fewer than 4 reflections per atom. In such cases first TLS model are 
refined, one-group-per-chain (yes, that has room for improvement) plus any 
user-provided grouping. The TLS model that performs best in refinement is then 
kept (or no TLS model at all if they don't work). Given this TLS model, the 
structure model is refined with isotropic B-factors and flat B-factors. Both 
refinement results are then tested by a program called "bselect" that performs 
the Hamilton test plus some fallback test. The "best" model is then chosen. If 
this involves isotropic B-factors, the B-factor restraint weight is then 
optimised.

Some stats:
Of the 1958 cases in the databank, 573 are refined with a flat B-factor model 
(2.9 reflections/atom on average), 520 with isotropic B-factors and 
tighter-than-default restraint weights (3.8 reflections/atom on average), 612 
with isotropic B-factors and looser-than-default weights (4.1 reflections/atom 
on average), the rest is isotropic with default weights (3.8 ref/atom). 

So there is a trend given the number of reflections per atom but it is not that 
strong for individual cases. Testing is needed. I won't claim that this is the 
best protocol for each of the cases, but I guess they are decent starting 
points for most. 

Cheers,
Robbie

> -Original Message-
> From: Tom Peat 
> Sent: Saturday, January 6, 2024 21:42
> To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten
> 
> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
> 
> It appears that Zhonghao might be worried about his data to parameter ratio.
> At 3 A, one can easily be in a situation where one has fewer reflections than
> four times the number of atoms (X, Y, Z plus B).
> I like the idea of starting out with the average B (or even Wilson B) and then
> doing TLS as that should reduce the number of parameters being refined.
> Best regards, tom
> 
> ____________
> 
> From: CCP4 bulletin board  on behalf of Robbie
> Joosten 
> Sent: Saturday, January 6, 2024 8:13 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
> 
>   You don't often get email from robbie_joos...@hotmail.com. Learn
> why this is important <https://aka.ms/LearnAboutSenderIdentification>
> 
> 
> One wonders who those "many people" are. You may not want to use them
> as your go-to reference for refinement techniques.
> 
> Anyway, Refmac cannot do grouped B-factor refinement, but you are not
> missing out on anything. As Eleanor implied, one-per-residue B-factors give
> unrealistic results. You are much better off using isotropic B-factors with 
> tight
> restraints (Refmac's default is already quite tight). Add TLS in your 
> refinement
> to see if that helps.
> If you have a really poor data/parameter ratio you could go for a flat 
> B-factor
> model and try to capture most of the B-factor in the TLS model. This is
> typically not needed at 3A, but there are exceptions (low solvent -more
> atoms-  or low completeness -fewer reflections- are factors to consider). If
> you do go for a flat B-factor model, you need to define sensible TLS groups.
> This takes some trial and error.
> 
> pdb-redo has decent algorithms to select the B-factor model and weight for
> Refmac. You could use that as a starting point for your model.
> 
> HTH,
> Robbie
> 
> 
> 
> On 6 Jan 2024 03:13, "chenzhonghao...@163.com"
>  wrote:
> 
> 
>   Dear Prof. Dr. Dodson and all CCP4 community,
> 
> 
> 
> Thanks for your reply.
> 
> 
> 
>Just now, I used baverage. I found that it can average the B factor but
> not refine it.
> 
> This function does not fit my requirement, because my resolution is
> low as 3 A.
> 
>Many people said that Refmac5 overrefines the structure if I used
> isotropic temperature refinement.
> 
> 
> 
>   Did refmac5 or other programs in CCP4 have similar functions like
> one_adp_group_per_residue or two_adp_groups_per_residue in Phenix?
> 
> 
> 
>Any help would be highly appreciated!
> 
> 
> 
> 
> 
> 
>   chenzhonghao...@163.com
> 
> 
>   From: Eleanor Dodson <mailto:176a9d5ebad7-dmarc-
> requ...@jiscmail.ac.uk>
>   Date: 2024-01-05 23:48
>   To: CCP4BB <mailto:C

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

[Robbie Joosten]

One wonders who those "many people" are. You may not want to use them as your go-to reference for refinement techniques.Anyway, Refmac cannot do grouped B-factor refinement, but you are not missing out on anything. As Eleanor implied, one-per-residue B-factors give unrealistic results. You are much better off using isotropic B-factors with tight restraints (Refmac's default is already quite tight). Add TLS in your refinement to see if that helps. If you have a really poor data/parameter ratio you could go for a flat B-factor model and try to capture most of the B-factor in the TLS model. This is typically not needed at 3A, but there are exceptions (low solvent -more atoms-  or low completeness -fewer reflections- are factors to consider). If you do go for a flat B-factor model, you need to define sensible TLS groups. This takes some trial and error.pdb-redo has decent algorithms to select the B-factor model and weight for Refmac. You could use that as a starting point for your model.HTH,RobbieOn 6 Jan 2024 03:13, "chenzhonghao...@163.com"  wrote:




Dear Prof. Dr. Dodson and all CCP4 community,
 
  Thanks for your reply.
 
 Just now, I used baverage. I found that it
can average the B factor but not refine it.
  This function does not fit my
requirement, because my resolution is low as 3 A. 
 Many people said that Refmac5
overrefines the structure if I used isotropic temperature refinement.
 
Did refmac5 or other programs in CCP4 have similar
functions like one_adp_group_per_residue or two_adp_groups_per_residue in Phenix?
 
 Any help would be highly appreciated!
 


chenzhonghao...@163.com
 From: Eleanor DodsonDate: 2024-01-05 23:48To: CCP4BBSubject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?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 atomsSYNOPSIS¶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  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] [pe...@leadszone.live: CCP4 Study Weekend-2024] (fwd)

[Robbie Joosten]

Hotel booking scammers for instance. Cheers,RobbieOn 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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Re: [ccp4bb] Alternatives to X

[Robbie Joosten]

Hi David,

Thank you for the Mastodon links. I like the idea of Mastodon, but many servers 
do blanket bans against other servers, particularly if these are very 
libertarian (e.g. have too much "Freeze Peach"). Your Mastodon 'heritage' seems 
to matter a lot. Nevertheless, it's good to see that engagement is growing. I 
find LinkedIn mostly useful for broadcasting, not really for engagement, so not 
really an X alternative.

Personally, I think it is a shame so many scientists left Twitter/X (or said 
they did/would). Especially if this is for activistic reasons. Yes, it is quite 
unfiltered nowadays, but I actually like to have things in the open whether I 
agree with them or not. It puts more responsibility on the community and the 
community notes help with that. Purely scientific posts don't seem to suffer 
from the new management and your timeline keeps having useful stuff as long if 
you actually engage with (not just follow) users of interest. I do use Twitter 
as a private person, not on behalf of my work. I wonder if that makes a 
difference to my experience.

It is important to note that many X alternatives are not available in the EU to 
avoid regulations (says something about those platforms). That makes Mastodon 
and X the only real options. That is, far behind the CCP4bb.

Cheers,
Robbie

  

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of David
> Briggs
> Sent: Wednesday, December 6, 2023 08:19
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Alternatives to X
> 
> Hi all,
> 
> I did a little (and entirely unscientific) test on this with one of our 
> recent papers.
> 
> Views : Linkedin came out on top.
> 
> Engagement from other scientists : Mastodon.
> 
> X didn't really do much, last I checked.
> 
> There is a structural biology community on Mastodon and there are several
> servers (a.k.a instances) that are science themed...
> 
> at_struct_dot_bio
> at_mstdn_dot_science
> at_biologists_dot_social
> at_cryoEM_dot_social
> at_qoto_dot_org
> at_fediverse_dot_science
> 
> Some suppliers are beginning to appear (e.g. Quantifoil) and there is a
> structural biology Mastodon group (struc...@a.gup.pe) that acts a bit like a
> distribution list.
> 
> Hth,
> 
> Contact me off list if I can help get you started.
> 
> Dave
> @xtald...@xtaldave.net
> 
> (Apologies if anyone got this twice - the original was pinged back as it 
> tripped
> the spam filter, presumably the list of servers)
> 
> 
> 
> 
> 
> Dr David C. Briggs CSci MRSB
> 
> Principal Laboratory Research Scientist
> 
> Signalling and Structural Biology Lab
> 
> The Francis Crick Institute
> 
> London, UK
> 
> ==
> 
> about.me/david_briggs 
> 
> 
> 
> From: CCP4 bulletin board  on behalf of Marc
> Graille 
> Sent: Wednesday, December 6, 2023 6:33:06 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Alternatives to X
> 
> 
> External Sender: Use caution.
> 
> Dear colleagues,
> 
> I take advantage of Tim's message about the fact that responsible people have
> resigned from X.
> I  really enjoyed Twitter (which I discovered rather late) because it was a 
> great
> tool for announcing news from my laboratory, but also for keeping abreast of
> recent publications or pre-publications related to my research interests.
> I notice that many scientists have deserted X in recent months.
> 
> Can anyone suggest user-friendly alternatives used by the scientific
> communities to announce recent publications or news in their fields?
> 
> Best wishes,
> 
> Marc
> —
> Marc GRAILLE, PhD
> DR1-CNRS
> Laboratoire de Biologie Structurale de la Cellule  (BIOC; Ex-Laboratoire de
> Biochimie)
> UMR7654 du CNRS
> 
> 
> Head of the team: “Translation and degradation of eukaryotic mRNAs”
> 
> 
> ÉCOLE POLYTECHNIQUE
> 91128 PALAISEAU CEDEX
> FRANCE
> : +33 (0)1 69 33 48 90
> 
> 
> 
>  : marc.grai...@polytechnique.edu   /
> Twitter : @GrailleLab 
> https://portail.polytechnique.edu/bioc/en/research/coupling-between-
> translation-and-mrna-degradation-eukaryotes
> —
> 
> 
> 
> 
>   Le 2 déc. 2023 à 10:15, Tim Grüne   > a écrit :
> 
>   Hi Mark,
>   responsible people are resigning from X.
>   Cheers,
>   Tim
> 
>   Am 01.12.2023 23:24, schrieb Mark J. van Raaij:
> 
> 
>   just came across this critique of that paper on Twitter:
>   This exciting paper shows AI design of materials, robotic
> synthesis.
>   10s of new compounds in 17 days. But did they? This paper has
> very
>   serious problems in materials characterisation. In my view it
> should
>   never have got near publication. Hold on tight let's take a look
> 
>   [1]
>   Robert Palgrave (@Robert_Palgrave) on X [1]
>   twitter.com   [1]
>   but I'm not enough of an 

[ccp4bb] Downtime for PDB-REDO, AlphaFill, DSSP and CCD.

[Robbie Joosten]

Dear CCP4 and CCPEM bulletin boarders,

Due to scheduled electrical maintenance at our host instate, our structural 
biology resources PDB-REDO (https://pdb-redo.eu), AlphaFill 
(https://alphafill.eu), DSSP (https://pdb-redo.eu/dssp) and CCD 
(https://ccd.rhpc.nki.nl/) will be harder to reach from Friday 3rd of November 
22:00h until Saturday 4th of November 16:00h (Amsterdam time). We will try to 
minimise the downtime. We apologise for the inconvenience.

Best wishes from our entire team,
Robbie Joosten



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Re: [ccp4bb] An unknown but strong positive electron density in my crystal

[Robbie Joosten]

I couldn't either. People should add pictures as attachements rather than pasting them inline. Cheers,RobbieOn 11 Aug 2023 19:08, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:Hmm - I cant see a picture..Your email has this..img src="">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

[Robbie Joosten]

Although the effect should be quite small, is the wavelength in your reflection 
file consistent with the actual wavelength? 

Another option is that specific filters on atom types were used in the TLS 
refinement. I would refine the models with another program 
(REFMAC/Buster/PDB-REDO) to see if the B-factor anomaly remains.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Daniel M.
> Himmel, Ph. D.
> Sent: Wednesday, August 2, 2023 17:06
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] High Temperature Factors with TLS
> 
> One possible explanation for high B-factors, assuming the coordinates are
> refined correctly, is partial occupancy and high mobility (dynamics) at those
> heavy atom sites.
> 
> Also, one should check Fo-Fc maps of those positions.  Are other atom types
> substituting for some of those heavy atoms (such as sulfate instead of
> phosphate)?
> 
> 
> Daniel
> 
> ___
> 
> Daniel M. Himmel, Ph. D.
> 
> Principal, Himmel Sci Med Com, LLC
> 
> E-mail:  danielmhim...@gmail.com
> 
> 
> URL   :  https://www.HimmelSciMedCom.com
> 
> 
> 
> On Wed, Aug 2, 2023 at 10:42 AM 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
> 
> 
> 
> 
> 
>   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] Binding affinity in AutoDock Vina

[Robbie Joosten]

Are you doing self-docking or are you analysing the models as-is? Not all binding poses in the PDB are realistic and things like atomic clashes have a massive energy penalty.Have you looked at the model in the electron density? You can also try the pdb-redo version op the same pdb entry to see if that gives a more sensitive binding energy.HTH,RobbieOn 28 Jun 2023 17:39, Thripthi Shenoy  wrote:I am performing docking studies for some of the protein structures from PDB using AutoDock Vina. Some of the ligands are giving binding energy as positive integers (eg. 435 kcal/mol). I tried rectifying the issue best to my knowledge. I would be grateful if someone could explain to me the reason for such a result.Thanking in advance,Thripthi S.


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Re: [ccp4bb] PDB redo R free

[Robbie Joosten]

To add to Tim's references, the algorithms that pdb-redo uses to deal with Rfree and possible bias are described here: https://journals.iucr.org/d/issues/2012/04/00/ba5174/index.htmlIf you happen to have a very small dataset (< 5000 reflections) pdb-redo does 10-fold cross validation and returns Rcomplete as well.Cheers,RobbieOn 28 Apr 2023 11:26, Tim Gruene  wrote:Dear Qixu Cai,

it  is a misconception that Rfree was not free anymore. The gap does
not close when you swap the reflections in Rfree set. The 'free'
reflections are freed when you do proper refinement, i.e., when the
value of the target function becomes stationary.
See https://doi.org/10.1107/S0907444997013875 and
https://doi.org/10.1107/S0907444999016868 for the mathematical
background, https://doi.org/10.1073/pnas.1502136112 for an experimental
treatment, and Ian Tickle's explanations on this topic here on the
CCP4bb.

Best wishes,
Tim


On Fri, 28 Apr 2023 16:54:07 +0800 Qixu Cai  wrote:

> Dear Robbie and Tim，
> 
> Thanks a lot for your reply. I just do not understand that if we can
> change the R free set during different rounds of refinement, the gap
> between Rwork and Rfree would be small, and Rfree would be
> meaningless, as R-free set is not "free".
> 
> Best regards,
> 
> Qixu Cai
> Email: caiq...@gmail.com
> 
> 
> 
> Robbie Joosten  于2023年4月28日周五
> 15:26写道：
> 
> > Hi Qixu,
> >
> > PDB-REDO tries to have a minimum number test set reflections to
> > reduce the error margin in R-free. As Tim says this is not a
> > problem but if you reach out privately we can change your
> > calculation to use your current testset. That is not recommended
> > though.
> >
> > Cheers,
> > Robbie
> >
> > On 28 Apr 2023 04:51, Qixu Cai  wrote:
> >
> > Dear all,
> >
> > I'm using the PDB-REDO server to refine my structure. I found that
> > PDB-REDO said that 5% R-free set is too small and it created a new
> > R-free set.
> >
> > Is possible for the PDB-REDO server to keep the original R-free set
> > to make final Rfree value comparable?
> >
> > Best regards,
> >
> > Qixu Cai
> > Email: caiq...@gmail.com
> >
> >
> > --
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >
> >  



-- 
--
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] PDB redo R free

[Robbie Joosten]

Hi Qixu,PDB-REDO tries to have a minimum number test set reflections to reduce the error margin in R-free. As Tim says this is not a problem but if you reach out privately we can change your calculation to use your current testset. That is not recommended though.Cheers,RobbieOn 28 Apr 2023 04:51, Qixu Cai  wrote:Dear all,I'm using the PDB-REDO server to refine my structure. I found that PDB-REDO said that 5% R-free set is too small and it created a new R-free set.Is possible for the PDB-REDO server to keep the original R-free set to make final Rfree value comparable?Best regards,Qixu CaiEmail: caiq...@gmail.com


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

[Robbie Joosten]

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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Re: [ccp4bb] Issue about cif file of ligand

[Robbie Joosten]

Dear Ning,

There is a separate bulletin board for anything Phenix. You can try the CCP4 
program AceDRG to generate restraint from a SMILES string. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ning Li
> Sent: Monday, April 3, 2023 18:17
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Issue about cif file of ligand
> 
> Hi everyone,
> 
> My crystal structure contains a ligand and I generated the cif file of the 
> ligand
> using phenix.elbow from the smiles file of the ligand. The ligand was drawn 
> and
> the smiles file was generated from
> https://pubchem.ncbi.nlm.nih.gov//edit3/index.html. My problem is that the
> double bond (shown in the picture) is longer than the single bond in the
> generated elbow pdb file. Although the bond can be recognized correctly in the
> Coot (display the correct double bond), the simulation software doesn't
> recognize them correctly because of the bond length. In my theory, the double
> bond of the ring should be shorter than the single bond, is there any reason
> why phenix elbow generate this or any parameters I can set to overcome this?
> Thank you for your suggestions.
> 
> Ning
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] new PDB file format

[Robbie Joosten]

WHAT_CHECK has a check for suspiciously rounded coordinates. I have never seen it triggered.Cheers,RobbieOn 3 Apr 2023 10:11, James Holton  wrote:
Thanks to everyone for being such good sports!

It is good to know that there is still room for good-natured funny
in what can be stressful times.

Truth be told, I actually did do some experiments rounding off PDB
coordinates to the nearest A.  You can try it with this one-line
shell command:
cat refined.pdb |\
awk '! /^ATOM|^HETAT/{print;next}\
  {X=substr($0,31,8);Y=substr($0,39,8);Z=substr($0,47,8);\
   pre=substr($0,1,30);post=substr($0,55)}\
  {X=sprintf("%.0f",X);Y=sprintf("%.0f",Y);Z=sprintf("%.0f",Z)}\
  {printf("%s%8.3f%8.3f%8.3f%s\n",pre,X,Y,Z,post)}' |\
cat > roundoff.pdb


  These rounded-off structures look ... weird. And yes they really
do crash validation programs.  Food for thought perhaps on what
"resolution", rmsd, and especially GDT_TS really mean?

-James Holton
MAD Scientist


On 4/1/2023 1:28 PM, Sweet, Robert
  wrote:


  Knowing the author as I do, I checked the date and time, and wasn't fooled.


From: CCP4 bulletin board  on behalf of Carter, Charlie 
Sent: Saturday, April 1, 2023 4:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] new PDB file format

I fell for this momentarily, hence compliments to James. I was fooled by the absolutely sensible intro.

Charlie


  
On Apr 1, 2023, at 12:34 AM, 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] [Sender Not Verified] Re: [ccp4bb] To Trim or Not to To Trim

[Robbie Joosten]

Hi Markus,

Just to make sure that things are clear: PDB-REDO adds missing side chains 
(that is a design choice) and it also adds missing loops if, and only if, there 
is a homologous template, there is sufficient density (although the criteria 
are rather forgiving), and the geometry of the loop stays okay upon real-space 
refinement. We do not build termini.

Your water example is a very nice one, this also happens for main chain atoms 
unfortunately. So unlike building parts of the protein that are chemically 
attached, please be careful with building waters. Only build ones that you are 
sure are waters. If you know that it is something else, but you don’t know 
what, please don’t build anything. I actually encourage students to build 
waters by hand. It is really simple and fast in Coot and it takes though a tour 
of you structure model enabling you to spot other issues.

HTH,
Robbie

From: CCP4 bulletin board  On Behalf Of Rudolph, Markus
Sent: Tuesday, March 14, 2023 15:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [Sender Not Verified] Re: [ccp4bb] To Trim or Not to To 
Trim

Hello Adrian,

Provided a crystal contains the intact protein, as measured by mass 
spectrometry of a washed and dissolved crystal, leaving out side-chains makes 
little sense, even if some of them are destroyed by X-rays during data 
collection. I realize that most of the time, no such analysis is done on 
crystals, but if you assume all residues are there, then they must fit into the 
asymmetric unit. This includes N- and C-terminal residues, loops, and any 
side-chains without density. If side-chains won't fit, e.g. by crashing into 
symmetry neighbors, then the main-chain trace is very likely wrong. Thus, 
placing side-chains in a model is a good test for a correct main-chain trace. I 
understand many protein architects out there omit the terminal extensions and 
longer loops, and so do I. pdb_redo will automatically complete a model, so one 
could say - don't bother, as a user I'll retrieve the re-refined model from 
there. This is not my personal choice of model building, but a practical option 
from the viewpoint of downstream users. Sometimes, however, I see models where 
side-chains are truncated but the little density still present for the 
side-chain is interpreted by water (see image attached, in which case the water 
comes from a symmetry-related position). If one says "don't build what you 
don't see but build what the data tell you", a well-intended but 
mis-interpreted water molecule may occupy the density belonging to a truncated 
side-chain. I as a user would be confused by this, especially when using such 
models for ligand binding studies where water is important. In our SBDD 
projects, we always take B-values into account, and we welcome complete models 
or we complete and re-refine them ourselves. So yes, my 12 points go to the 
"let the B-factors take care of it” song. But really, I'm thankful for _any_ 
published structure, even with sup-optimal parameterization, experienced 
structural biologists can deal with that and communicate the information to 
their collaborators.


...which brings up the other evergreen, whether the PDB should be more strict 
about ...



Best wishes,
Markus



On Fri, Mar 10, 2023 at 5:33 PM Goldman, Adrian 
mailto:adrian.gold...@helsinki.fi>> wrote:
Maybe simplest just to trim it back. I do worry that the presence of a wrong 
conformation will lead to inaccurate vdw clashes that could negatively affect 
other atoms.

Sent from my iPhone

> On 10 Mar 2023, at 18:25, Phil Jeffrey 
> mailto:pjeff...@princeton.edu>> wrote:
>
> On 3/10/23 4:05 AM, Julia Griese wrote:
>> Hi all,
>> My impression has been that the most common approach these days is to “let 
>> the B-factors take care of it”, but I might be wrong. Maybe it’s time to run 
>> another poll?
>> Personally, I call any other approach R-factor cosmetics. The goal in model 
>> building is not to achieve the lowest possible R-factors, it’s to build the 
>> most physically meaningful, most likely to be correct, model.
>
> And I could call your approach "model cosmetics".
>
> If you can't see the side-chain, you don't know where it is and you probably 
> don't even know where the centroid of the distribution is. Only in the case 
> of very short side-chains with few rotamers can you make a reasonable volume 
> approximation to where the side-chain is and "let the B-factors" smear out 
> the density to cover a range of the projected conformations.
>
> For longer side-chains, if you put it in a single conformation, you are very 
> likely NOT coming close to correctly modeling the actual distribution of the 
> conformations.  So let's circle back on "most likely to be correct model" and 
> ask what we *actually* know about where the atoms are.
>
> Put your disordered Arg in with 10 alternate conformations, each with a 
> refined relative occupancy, and then let the B-factors smear that lot out, 
> and that's your better 

Re: [ccp4bb] Unidentified density

[Robbie Joosten]

This is always hard to see this way, but it looks like glycerol at first 
glance. Try to fit that.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of zeyaul
> islam
> Sent: Tuesday, February 21, 2023 12:13
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Unidentified density
> 
> Dear all
> 
>  We have solved the structure of nanobody at 1.25 angstrom. We observe some
> unidentified density near the serine. Please have a look at the figures. 
> Protein
> was purified in PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2
> mM KH2PO4) and the crystallisation condition has 0.1 M BIS-TRIS pH 5.5, 2.0 M
> ammonium sulfate. Any ideas what this could be? I tried SO4 and PO4 but
> didn’t satisfy the observed electron density.
> 
> I appreciate any help you can provide.
> 
> Thanks
> 
> Zeya
> 
> Zeyaul Islam, PhD
> 
> QBRI - Qatar Biomedical Research Institute
> 
> P.O. Box: 34110
> Doha – Qatar
> 
> Tel: +974 445 46690
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Fill-your-own-model with AlphaFill and other updates

[Robbie Joosten]

Dear bulletin boarders,

The previous version of this post did not come through. Apologies if this turns 
out to be a double post.

To celebrate the publication of our AlphaFill paper 
(https://www.nature.com/articles/s41592-022-01685-y), we have released a new 
version of our https://alphafill.eu website. It has some (we hope) useful new 
features:
- AlphaFold V3 and V4 entries (all Uniprot entries) are now available. When you 
ask for them, the AlphaFold model is downloaded through the 3D-Beacons system 
and filled on-the-fly.
- You can download AlphaFill entries with your personal selection of 
transplants. The download button is above the transplant selection boxes.
- Fill-your-own-model is now available for any structure model (computational 
or experimental). Just upload a valid mmCIF or PDB file and it will look for 
potential ligands ions and cofactors. This feature is completely new and 
constructive feedback is always appreciated. 

All the best,
Maarten, Ida, Robbie and Tassos



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[ccp4bb] Fill-your-own-model with AlphaFill and other updates

[Robbie Joosten]

Dear bulletin boarders,

To celebrate the publication of our AlphaFill paper 
(https://www.nature.com/articles/s41592-022-01685-y), we have released a new 
version of our https://alphafill.eu website. It has some (we hope) useful new 
features:
- AlphaFold V3 and V4 entries (all Uniprot entries) are now available. When you 
ask for them, the AlphaFold model is downloaded through the 3D-Beacons system 
and filled on-the-fly.
- You can download AlphaFill entries with your personal selection of 
transplants. The download button is above the transplant selection boxes.
- Fill-your-own-model is now available for any structure model (computational 
or experimental). Just upload a valid mmCIF or PDB file and it will look for 
potential ligands ions and cofactors. This feature is completely new and 
constructive feedback is always appreciated. 

All the best,
Maarten, Ida, Robbie and Tassos




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[ccp4bb] AlphaFill and PDB-REDO downtime this Friday and Saturday

[Robbie Joosten]

Dear CCP4bb-ers,Due to construction and electrical maintenance work, AlphaFill, PDB-REDO and all related services will be down or poorly reachable between 18:00h CET November 4th and 12:00h November 5th.My apologies for the inconvenience.Best wishes,Robbie


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Re: [ccp4bb] bond angle deviation listing in refmac log

[Robbie Joosten]

Hi Garib,

> Are these related to the side chain of ARG? In the monomer library sigmas are
> capped from below - 1.5degree.
> In the PDB these sigmas might be very small and tiny differences could be 
> given
> as outliers.
> Another reason might be that in the monomer library these two angles are
> identical (they are considered graph-equivalent, however, rotating around NE-
> CZ may make them non-equivalent in 3D space):
> ARG NE CZ NH1 120.052 1.50
> ARG NE CZ NH2 120.052 1.50
The chi-5 angle is not really freely rotatable due to the 1.33 bond order. It 
does give away more than say, a peptide bond with 1.5 bond order. Anyway, NH2 
and NH1 have E/Z differences if you assume the bond is not freely rotatable.

> In the PDB they may be considered different with small differences and very
> small sigmas.
I'm using
ARG NE CZ NH1 121.5 1.00
ARG NE CZ NH2 119.2 0.90

From https://pubmed.ncbi.nlm.nih.gov/27326702/

> I personally do not think that these differences are significant or important.
> However, to make pdb validation happy you can change the sigmas and make
> the angles different. Then NH1 and NH2 will become inequivalent and you have
> to change your coordinates (it could be done automatically if somebody writes
> a tiny program)
Because chi-5 was freely rotatable in O (against convention) there is a check 
for this in WHAT_CHECK. AFAIK the atom naming is fixed in pdb-redo based on 
that. We can build in into flipper.

Cheers,
Robbie

> 
> If the problem is not related with this then I need more info.
> 
> Regards
> Garib
> 
> 
> 
>   On 20 Oct 2022, at 12:33, Bernhard Rupp
> mailto:hofkristall...@gmail.com> > wrote:
> 
>   Hi Fellows/Garib,
> 
>   I notice unexplained discrepancies between the PDB validation report
> and the Refmac log file:
> 
>   a.  If I set in  ‘Monitoring and Output Options’ the angle sigma for
> the log output reporting option to the PDB 5 sigma cutoff,
> 
>   I get zero angle deviations (i.e., no angle deviation printout at all 
> in the
> log), even at improbably low sigma levels such as 2.0 or 1.0
> 
>   monitor MANY torsion 5.0 distance 5.0 angle 1.0 plane 5.0
> 
> 
>   b.  PDB informs me that there are up to 10 sigma outliers on
> multiple (and almost exclusively) ARG N-C-N angles (how to fix this we address
> later).
> 
> 
>   Garib, I can send you a link to the complete log, below the header for
> versions (windows) :
> 
>   #CCP4I VERSION CCP4Interface 8.0.005
> 
>   #CCP4I SCRIPT LOG refmac5
>   #CCP4I DATE 20 Oct 2022  13:17:07
>   #CCP4I USER 'UNKNOWN'
>   #CCP4I PROJECT data_mono
>   #CCP4I JOB_ID 13
>   #CCP4I SCRATCH C:/Users/br/AppData/Local/Temp
>   #CCP4I HOSTNAME BR-WORK
>   #CCP4I PID 10064
> 
>   
> 
>   
>   
>   
> 
> 
> 
> ###
>   
> ###
>   
> ###
>   ### CCP4 8.0.005: Refmac  version 5.8.0352 : 05/31/22##
>   
> ###
> 
>   Thx, BR
>   -
>   Bernhard Rupp
>   k.k. Hofkristallamt
>   001 (925) 209-7429
>   +43 (676) 571-0536
>   b...@ruppweb.org 
>   hofkristall...@gmail.com 
>   http://www.hofkristallamt.org/ 
>   -
>   Doors and corners – that’s where they get you
>   -
> 
> 
> 
> 
> 
> 
> 
>   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] PAIREF, Anisotropy and STARANISO

[Robbie Joosten]

The combination of paired refinement and anisotropy should not be a problem, 
but I think there are a few catches depending on the implementation. I'll 
reason from the PDB-REDO implementation of paired refinement which was made 
assuming a "you get what you get" set of reflections without the option of 
reprocessing. This can include datasets that are severely anisotropic with 
isotropic cut-off at the highest resolution direction, datasets in which the 
detector was too close so there are missing reflections in a systematic (but 
not ellipsoidal, right?) way, and sets with missing wedges, shells, or random 
sets (e.g. the test set) of reflections that could have been observed/deposited.

To me, paired refinement is a very elegant way to find out whether an 
additional set of (higher resolution) reflections caries information that a 
refinement program can use to improve its results. Its introduction (thanks, 
Kay) is a big step forward on the eternal discussions on resolution cut-offs. 
There need not be any assumption of (an)isotropy at this stage. In the pdb-redo 
implementation we do make another assumption: the higher the resolution, the 
noisier the data gets. That is, that usable information per reflection 
gradually goes down with resolution. 

This has a consequence for how to chose your resolution steps in refinement 
(IMO). To make sure the useful information content per step goes down, you 
shouldn't use equal steps in resolution or any other type of binning that 
results in unequal numbers of reflections per step. Instead taking steps of 
equal numbers of reflections assures that the steps become gradually worse in 
terms of usability. The added bonus is that steps of equal numbers of 
reflections also ensure that each step has a very similar number of test set 
reflections which are needed for establishing the final resolution cut-off. The 
only real exception I can think of is when one step happens to have a serious, 
but untreated, ice ring and the next one doesn't. 

In practice, this approach works well and we see that paired refinement is a 
very popular option in pdb-redo (10% of the calculations include paired 
refinement at request of the users). It has been used a lot to 'shut up referee 
#2' at the review stage, but also in the early stages of model building. I 
really recommend against that as refinement is just less stable at that stage 
and the distinction between resolutions steps is small at best. Anyway, I think 
there is little to no need to make assumptions about data (an)isotropy in 
paired refinement, but one could make a case for a STARANISO-like approach or 
any other anisotropic selection of 'observed' reflections. You 'poison' your 
resolution steps less with reflections that carry only noise. Whether this 
affects the chosen resolution cut-off in any meaningful way is yet to be 
determined (happy to help with that). That said, I do agree with the previous 
posts that you shouldn't treat your data in any other way than selection.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kay
> Diederichs
> Sent: Thursday, October 6, 2022 12:33
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] PAIREF, Anisotropy and STARANISO
> 
> Dear Gerard,
> 
> I'm not going to comment on what others said in this (new) thread; just trying
> to make a few remarks about what you write below -
> 
> On Tue, 4 Oct 2022 17:01:10 +0100, Gerard Bricogne
>  wrote:
> 
> >Dear all,
> >
> > First of all, apologies for breaking the threads entitled "PAIREF -
> >Warning - not enough free reflections in resolution bin" and "Anisotropy" by
> >merging them into a new one, but it somehow felt rather against nature to
> >keep them separate.
> >
> > Since the early days of the availability of STARANISO [1] (the actual
> >starting year for the Web server [2] was 2016), we had a hunch that much of
> >what was happening in the PAIREF procedure might simply be the detection of
> >the existence of significant data beyond an initially chosen resolution
> >cut-off not only as a result of an excessively conservative criterion having
> >been applied in that initial choice, but as a consequence of anisotropy in
> >the data.
> 
> Why "much of what was happening ... as a consequence of anisotropy"? These
> words imply that datasets where PAIREF indicates "existence of significant 
> data
> beyond an initially chosen resolution cut-off" (EOSDBAICRC) are anisotropic,
> but that is a) not the case, because PAIREF - or paired refinement in general 
> - in
> my experience, and that of others, often indicates EOSDBAICRC also for
> isotropic data, b) this depends on the initial cutoff. So your general 
> statement
> (or hunch?) cannot be correct.
> 
> > The latter would give rise to different diffraction limits in
> >different directions, and the choice of a single value for "the resolution"
> >at which the data were cut off would necessarily yield a compromise value
> >between 

[ccp4bb] Problem downloading models maps in from PDBe in Coot

[Robbie Joosten]

Not sure if this is a PDBe bug or a Coot bug (or a combination thereof)...

I'm using the latest WinCoot in CCP4 8.0. When I try to 'Fetch PDB using 
Accession Code', I do not get any models so I guess the target URL is wrong. 
When I use Fetch PDB & Map using EDS, I sometimes get a map (1cbs, 3fvl), 
sometimes I don't (1ctn, 1lee and many more). All of these maps used to be 
available and PDB-REDO versions of all these entries exist. Does anyone know 
what is going on?

Cheers,
Robbie



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Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

[Robbie Joosten]

Hi Pavel,

There are a number of DNA structures that are complete made up out of alternate 
atoms.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Pavel
> Afonine
> Sent: Wednesday, August 24, 2022 00:02
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] ISO model with large groups of atoms in alternative
> conformations
> 
> Dear community,
> 
> 
> 
> I’m looking for an example of a crystal structure where a large group of
> atoms (as large as a whole chain or even a domain) have more than one
> distinct conformation that would require modeling of such chain/domain as
> more than one individual copy, with each copy having partial occupancy. I’m
> not sure if that even exists but if someone can share an example that'd be
> very much appreciated!
> 
> 
> 
> Thanks!
> Pavel
> 
> 
> 
> 
> 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] Polymer ligand (Jefffamin) modeling in low resolution maps

[Robbie Joosten]

Hi Jan,

I would advise against playing with occupancies because it adds a complication 
that has side effects on the density and is easily overlooked by the users of 
your model. There are many Jeffamines on the market, so figuring out which is 
the one you have is the first step. Depending on how much effort you want to 
put in you can do the following:
- Figure out the register of the oxygens if the density allows you to place 
atoms (i.e. it is not a tube without peaks). I would use a PEG molecule for 
this. If you have no meaningful contacts you can refine alternative models and 
see which refines best. There are just three options.
- The next step depends on the type of jeffamine you have. If it is just blocks 
of propylene glycol. You have two options for the methyl group register. You 
can try both. If it is a mixture of ethylene and propylene glycol blocks, this 
is where I would give up and not place any methyls unless they are really 
obvious. 
- Depending on the size of your blob and the type of Jeffamine you may, or may 
not see the termini of you molecule and you can try to model those.

If this all is a bit much for your project you can do the 'UNL' trick and just 
refine a string of carbons and explain what you did in the paper and model 
annotation.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Jan
> Stransky
> Sent: Friday, August 19, 2022 15:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution
> maps
> 
> Hi Matthew,
> 
> thanks for the thought.
> 
> Yes, I agree, that it is average whole lot of conformations. I am aware of
> FEMs, it is great tool, but I got similar results as with Polder maps.
> 
> Modelling just the "main chain" and calling it Jeffamin, is also an option I 
> was
> considering. It is part of the question, how to do properly for the PDB
> deposition. If I do just the Jeffamin "mainchain", it would be effectively PEG
> library, but not named as PEG. I think that would be confusing.
> 
> However, really treating it as aa residue with invisible sidechain is 
> interesting
> option. Our lab consensus is to keep the atoms, but reduce occupancy to
> almost 0. I think, I could do that for the methyl groups in Jeffamin.
> 
> Best regards,
> 
> Jan
> 
> 
> 
> 
> 
> On 8/19/22 11:42, Matthew Snee wrote:
> 
> 
>   Hi
> 
>   It is likely that your density is a consensus of multiple different
> jeffamines binding at different rotational orientations, so that at 2.6A the
> methyl groups are essentially averaged out, and therefore the density may
> not exist to be found.
> 
>   Phenix has a tool called "feature enhanced maps" which is designed
> to reverse the flattening of weak features, but I find its important to have
> the best possible phases (I.E most accurate model) before using it.
> 
>   I suppose you could model jeffamine, and delete the methyl groups
> (I.E treat is like a residue with an unresolved sidechain).
> 
>   Cheers
> 
>   Matthew.
> 
> 
>   From: CCP4 bulletin board 
>   on behalf of Jan Stransky
>  
>   Sent: 18 August 2022 10:37
>   To: CCP4BB@JISCMAIL.AC.UK 
>  
>   Subject: [ccp4bb] Polymer ligand (Jefffamin) modeling in low
> resolution maps
> 
> 
>   Dear all,
> 
>   we have a structure at not the greatest resolution (~2.6A) of which
>   crystal was grown in crystallization condition with Jeffamin. In the
>   maps, we see typical  PEG-like sausages. Jeffamin is basically a PEG
>   decorated with some methyl groups and it is terminated with amine
> groups.
> 
>   Now, the question is how to interpret such blobs? To my
> understanding
>   the methyl decoration is not regular, and it is not obviously visible in
>   the maps. Nor is clear, if there is a contact to the amine group. When
>   we tried to put in PEG models as placeholders, it explains the density
>   fine, but the contacts  are nothing great, e.g. position of the oxygens
>   in the polymer is  not clear.
> 
>   Calculating Polder maps does not clear things  up.
> 
>   How would you deal with interpretation such maps?
> 
>   Thank you for your ideas :-)
> 
>   Jan
> 
>   
> 
> 
>   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
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> 
> 
> 
> 
> 

Re: [ccp4bb] PDB to AlphaFold via Uniprot

[Robbie Joosten]

Hi Paul,

From the PDB file get the Uniprot primary accession code (see DBREF) and use 
this to get the Alphafold model using 3D-beacons 
(https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/).
You can also use 3D-beacons to get the related AlphaFill model (just saying...).

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Paul
> Emsley
> Sent: Friday, July 29, 2022 20:31
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] PDB to AlphaFold via Uniprot
> 
> I wonder if others are curious about (or know how to solve) the
> following problem:
> 
> I am looking at a PDB file that I've downloaded from a wwPDB site and I
> would like to see the AlphaFold model(s) overlaid. What the best (or
> easiest) way of doing that? (let's imagine that I can do a bit of
> scripting in python (including urllib) and can use the functions in Coot
> for the superposition).
> 
> Thanks,
> 
> 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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Re: [ccp4bb] Checking X-ray sequence (no more protein).

[Robbie Joosten]

Hi Jon,

There are placeholders for ASP/ASN and GLU/GLN ambiguities: ASX and GLX 
respectively. You can just use those. AFAICT there no such thing for VAL/THR 
ambiguities. You could look for the most likely canadidata based on multiple 
sequence alignments. Refinement of both alternatives can give hints in 
B-factors and if you are lucky in difference density. But if hydrogen bonding 
gives no hints, then the residues are also not in a place where the identity 
really matters. You can give your best guess with a CAVEAT record or use the 
name UNK to indicate that you do not know what the residue is. You would loose 
the knowledge that it is either VAL or THR in that case. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Jon
> Cooper
> Sent: Friday, July 29, 2022 12:14
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Checking X-ray sequence (no more protein).
> 
> Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray
> sequence for a protein where it is impractical to do experimental sequencing,
> protein or DNA. The structure refines to publishable R/R-free and the main
> ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where alternative H-
> bonding networks are possible. Running alpha-fold seems an interesting
> option? Any suggestions much appreciated.
> 
> Cheers, Jon.C.
> 
> Sent from ProtonMail mobile
> 
> 
> 
> 
> 
> 
> 
> 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] Missing double bonds in the ligand

[Robbie Joosten]

Dear Anil,Bond orders are not captured in PDB files explicitly. The way bonds are shown depends on the program and possibly additional information sources (i.e. molecular restraint or topology files). So this is just a "problem" with Schrödinger.Cheers,RobbieOn 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka"  wrote:Dear CCP4 Users,We are working on a ligand-bound structure and would like to look at protein-ligand interactions using Schrodinger.Molecule structure is: When we load the ligand-fitted PDB file into Schrodinger, the molecule appears to be flat like it should be in the structure but it removed all the double bonds in the ligand where the above shown original molecular structure has double bonds in it.When we load the same PDB file into pymol and look at the ligand it shows correctlyWe would appreciate if any insight or suggestions for why this may be happening and how to ensure the ligand shows properly when the PDB is loaded into Schrodinger. Would this be an issue with Schrodinger software or with the PDB file?I can be available by direct email for troubleshooting at amara...@purdue.edu.-- Anil Kumar Marapaka, Ph.D.Post-Doctoral Research Associate Department of Medicinal Chemistry and Molecular Pharmacology (MCMP),
Purdue University, West lafayette,Indiana-47907, USA.Mobile 1: +1-765-409-6245 (USA)Mobile 2: +91-995-998-5571 (India)Email 1: amara...@purdue.eduEmail 2: anilmarap...@gmail.com


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Re: [ccp4bb] Easy/Silly question

[Robbie Joosten]

BMA is mannose, not maltose

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Krieger,
> James M
> Sent: Friday, July 1, 2022 09:59
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Easy/Silly question
> 
> How about BMA for beta-D-maltose?
> 
> 
>   On 1 Jul 2022, at 05:55, Nigel Moriarty  wrote:
> 
> 
> 
>   
>   Yes, MAL was obsoleted about 2 years ago.
> 
>   Cheers
> 
> 
>   Nigel
> 
> 
>   ---
>   Nigel W. Moriarty
>   Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>   Lawrence Berkeley National Laboratory
>   Berkeley, CA 94720-8235
>   Phone : 510-486-5709 Email : nwmoria...@lbl.gov
>   Fax   : 510-486-5909  Web  : CCI.LBL.gov
>  bl.gov%2F=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec94d171
> a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C6
> 37922481423292553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwM
> DAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7
> C=PlWqacZfxRwjFqAdkMmtlz92YFpBwhFRBxa13p4wFx4%3D
> d=0>
>   ORCID : orcid.org/-0001-8857-9464
>  id.org%2F-0001-8857-
> 9464=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec94d171a470
> 8da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C63792
> 2481423292553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiL
> CJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C
> data=cOI56DuPY4K95dxf0HIIfAZ7mgoLvLLCxD7M%2BXjqa4g%3D=
> 0>
> 
> 
> 
>   On Thu, Jun 30, 2022 at 9:26 PM Diana Tomchick
>   > wrote:
> 
> 
>   It's GLC
> 
>   otherwise known as 4-ortho-alpha-D-Glucopyranosyl-D-
> glucose.
> 
>   See PDB ID 1ANF
> 
>   also
> 
>   https://en.wikipedia.org/wiki/Maltose
>  wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
> 
> 
>  wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
> Maltose - Wikipedia
>  wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
> Maltose (/ ˈ m ɔː l t oʊ s / or / ˈ m ɔː l t oʊ z /), also known as 
> maltobiose or
> malt sugar, is a disaccharide formed from two units of glucose joined with an
> α(1→4) bond.In the isomer isomaltose, the two glucose molecules are joined
> with an α(1→6) bond.Maltose is the two-unit member of the amylose
> homologous series, the key structural motif of starch.When alpha-amylase
> breaks ...
> en.wikipedia.org
>  wikipedia.org%2F=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec
> 94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C
> 0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4w
> LjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C
> %7C%7C=q6tgL29oHtiVRlDicK39FdGgKI3JcDyUXHxxfLLBfAA%3D
> rved=0>
>   Diana
> 
> 
>   **
>   Diana R. Tomchick
>   Professor
>   Departments of Biophysics and Biochemistry
>   UT Southwestern Medical Center
>   5323 Harry Hines Blvd.
>   Rm. ND10.214A
>   Dallas, TX 75390-8816
>   diana.tomch...@utsouthwestern.edu
>   (214) 645-6383 (phone)
>   (214) 645-6353 (fax)
> 
> 
>   From: CCP4 bulletin board   > on behalf of Joel Tyndall
> mailto:joel.tynd...@otago.ac.nz> >
>   Sent: Thursday, June 30, 2022 10:50 PM
>   To: CCP4BB@JISCMAIL.AC.UK
>     >
>   Subject: [ccp4bb] Easy/Silly question
> 
> 
> 
> 
>   EXTERNAL MAIL
> 
> 
> 
>   Hi folks,
> 
> 
> 
>   I 

Re: [ccp4bb] Regarding R factor value

[Robbie Joosten]

Depending on how you process the model, the reported R-value becomes invalid. 
So you need to get it from the PDB entry before processing or recalculate it 
with respect to the experimental data.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of
> Abhilasha Thakur
> Sent: Wednesday, June 1, 2022 07:52
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Regarding R factor value
> 
> Hello!!
> 
> I have 1500 processed PDB files and I need the R factor value for each pdb
> files. How I get this R factor value, because it's there initially but, after
> processing, some data from PDB is deleted. Manually to get R factor is not
> possible.
> 
> Please suggest me, how to get this R factor value for the entire PDB ids.
> 
> 
> 
> 
> 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] Problem with understanding mtz and hkl files of S SAD data

[Robbie Joosten]

mtzdump is a command line tool, so you have run it from a terminal. There is 
also a shorthand version for lazy people like me (notice the missing 'u'): 
mtzdmp something.mtz

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of
> Rituparna Saha
> Sent: Tuesday, May 10, 2022 14:51
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD
> data
> 
> Thank you for the suggestions. I had searched the mtzdump in CCP4i, but
> didn't find any, I only found the mtz2various program.
> 
> I am using the Shelxc/d/e suite. I had converted the ASCII.HKL file (the one
> that I had mentioned before) to mtz using Pointless. Then, when I used this
> file to run Shelxc/d/e, the job failed and I encountered errors each time. For
> this reason, I wanted to view and analyze the mtz file and HKL file. I donot
> know how to solve this problem as well.
> 
> Kindly guide me if I went wrong anywhere here.
> 
> 
> On Tue, May 10, 2022 at 5:49 PM Pedro Matias   > wrote:
> 
> 
>   Hi there,
> 
>   I assume you processed the data with XDS. If so, you can use xdsconv
> to convert the file other formats, including mtz
> 
>   To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is
> a format conversion program, just like xdsconv. You can convert directly to
> SCALEPACK format without a USER FORMAT option, and the output from a
> .sca file created from an mtz file with MTZ2various looks like this:
> 
> 
> 
>   1
>-987
>  105.79462.940   110.05090.000   105.00890.000 c 
> 1 2
> 1   <-- cell parameters and SG info
>-73   1   3 5.1 5.1 7.5 4.5 <--- h,k,l, I+, 
> sigI+, I-, sigI-
> (bijvoet mates)
>-73   1   4-1.4 6.8 3.4 5.3
> 
> 
> 
>   What is the software you are using to solve the structure via S-SAD? I
> recomment the shelxc/d/e suite that can be easily run via the hkl2map GUI.
> 
> 
> 
>   Best,
> 
>   Pedro
> 
> 
>   Em 10/05/2022 12:51, Rituparna Saha escreveu:
> 
> 
>   Dear all,
>   I am trying to solve a protein structure via S SAD phasing. I
> have the ASCII.HKL file, but whenever I opened the text file I couldn't
> understand which one is the F+ and F- values.
> 
>   Also, how can I read and analyze an mtz file? I tried using the
> MTZ2VARIOUS program in CCP4, where I changed it into USER FORMAT, it
> generated a .sca file, and the text file so generated did not have any labels
> (headers) inside it. It just gave me a list of values.
> 
>   Kindly guide me through this since I am really a novice in this
> field.
> 
>   --
> 
>   --
> 
>   -
> 
>   Regards,
>   Rituparna Saha
> 
>   Research Scholar
>   Bioseparation and Structural Biochemistry Lab
>   Department of Biotechnology, IIT Kharagpur
> 
> 
> 
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-bin/WA-
> JISC.exe?SUBED1=CCP4BB=1
> 
>   --
>   Industry and Medicine Applied Crystallography
>   Macromolecular Crystallography Unit
>   ___
>   Phones : (351-21) 446-9100 Ext. 1669
>(351-21) 446-9669 (direct)
>Fax   : (351-21) 441-1277 or 443-3644
> 
>   email : mat...@itqb.unl.pt 
> 
>   http://www.itqb.unl.pt/research/biological-chemistry/industry-and-
> medicine-applied-crystallography
>   http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> 
>   Mailing address :
>   Instituto de Tecnologia Quimica e Biologica António Xavier
>   Universidade Nova de Lisboa
>   Av. da República
>   2780-157 Oeiras
>   PORTUGAL
> 
>   ITQB NOVA, a great choice for your PhD
>   https://youtu.be/de6j-aaTWNQ
> 
>   Master Programme in Biochemistry for Health
>   https://youtu.be/UKstDCFjYI8
> 
> 
> 
> --
> 
> --
> 
> -
> 
> Regards,
> Rituparna Saha
> 
> Research Scholar
> Bioseparation and Structural Biochemistry Lab Department of Biotechnology,
> IIT Kharagpur
> 
> 
> 
> 
> 
> 
> 
> 
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Re: [ccp4bb] Regarding File conversion

[Robbie Joosten]

cif2pdb will do the trick if conversion is all you need. I use mmCQL to first 
rename 'chains' before converting. For both see: 
https://github.com/PDB-REDO/cif-tools

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Frederic
> Vellieux
> Sent: Tuesday, April 19, 2022 15:56
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Regarding File conversion
> 
> Hi,
> 
> Last time I needed to do this the most convenient for me was to use Coot,
> with a very large coordinate file. Coot pre v1 (v0 something) to read in
> coordinates in the mmcif format and write out coordinates in the PDB
> format.
> 
> HTH,
> 
> Fred.
> 
> On 2022-04-19 14:01, Abhilasha Thakur wrote:
> > Hello!!
> > Greeting of the day,
> >
> > I want to know regarding file conversion from mcif file format to PDB
> > format of proteins.
> > Is there any program or software that can be used to change one format
> > to another format. KIndly guide me about programs used for file
> > conversion or any other medium like python script or R script to
> > convert the file format without changing the coordinates  of the file.
> >
> >
> > Thankyou
> >
> > -
> >
> > 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:
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Re: [ccp4bb] Add secondary structure definition into an alphafold PDB

[Robbie Joosten]

Dear Ines,

The latest version of DSSP (https://github.com/PDB-REDO/dssp) also annotates 
the coordinate file in pdb or mmCIF. Note that mmCIF is preferred as you can do 
a more complete annotation. The latest version of mkdssp will be in CCP4 
version 8.

Cheers,
Robie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of
> Munoz.Ines
> Sent: Thursday, April 7, 2022 10:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Add secondary structure definition into an alphafold PDB
> 
> Harry, you are right! It was the first program that I used but as long as I 
> have
> seen it gives you the info regarding the amino acids that form those areas but
> then you have to include this info into your pdb manually.
> Best
> Inés
> 
> 
> > El 7 abr 2022, a las 10:29, Harry Powell - CCP4BB <193323b1e616-
> dmarc-requ...@jiscmail.ac.uk> escribió:
> >
> > CAUTION: This email originated from outside of the organization. Do not 
> > click
> links or open attachments unless you recognize the sender and know the
> content is safe
> >
> >
> >
> > Hi Ines
> >
> > DSSP? (In ccp4 as “mkdssp” in $CBIN)? Should work with any (valid??) PDB
> file
> >
> > “Oldie but goodie”...
> >
> > Harry
> >
> >> On 7 Apr 2022, at 09:24, Munoz.Ines  wrote:
> >>
> >> Dear all,
> >>
> >> Is there any program or server that automatically assign the secondary
> structure elements into a pdb generated by alpha fold?
> >>
> >> Many thanks
> >> Inés
> >>
> >>
> >>
> >>
> >> Inés G. Muñoz
> >> Head of Crystallography and Protein Engineering Unit
> >> Spanish National Cancer Research Centre, CNIO
> >>
> >> imu...@cnio.es
> >> Phone +34 91 732 8000 (ext. 3020)
> >>
> >> Melchor Fernández Almagro, 3
> >> 28029 Madrid, Spain
> >> www.cnio.es
> >>
> >>
> >> 
> >>
> >>
> >>
> >>
> >>
> >>
> >> Fb Amigos del CNIO |  Tw @CNIOStopCancer |  Youtube canalcnio
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> >>
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Re: [ccp4bb] sftools

[Robbie Joosten]

Hi Eleanor,

I actually add the wavelength to an mtz file with CAD:

  cad \
  HKLIN1 $WORKDIR/raw_nowavel.mtz \
  HKLOUT $WORKDIR/raw.mtz \
<> $WORKDIR/mtz_creation.log
LABIN FILE 1  ALLIN
DWAVELENGTH FILE_NUMBER 1 1 $WAVELENGTH
END
eof

I have no experience adding dataset names as these are inherited from the mmCIF 
reflection files I use.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Eleanor
> Dodson
> Sent: Tuesday, April 5, 2022 15:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] sftools
> 
> 
> 
> Does ANYONE know how to use this useful but ultra-frustrating program??
> 
> I have an mtz file which lacks WAVElength AND Dataset name.
> 
> I try to follow the sftools documentation, and get an output file which -
>  lacks WAVElength AND Dataset name.
> 
> 
> G
> 
> 
> sftools < 
> READ "detwin_job1-IMEANa.mtz" mtz
> SET DWAVE 1.2 WAVElength AND Dataset name.
> write "detwin_job1-IMEANab.mtz" mtz
> EXIT
> YES
> eof
> 
> 
> 
> 
> 
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Re: [ccp4bb] off topic -- pymol error message

[Robbie Joosten]

This means that you have an O-umlaut in your PDB file. That should never 
happen! PDB files should only have basic ASCII characters, not UTF-8. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of 陈成
> Sent: Tuesday, April 5, 2022 13:12
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] off topic -- pymol error message
> 
> Hi all,
> 
> What does this message means when loading a pdb file in pymol:
> 
> 'utf-8' codec can't decode byte 0xd6 in position 37: invalid continuation byte
> 
> Thank you!
> 
> Chen
> 
> 
> 
> 
> 
> --
> Cheng Chen, Associate Professor
> 
> School of Life Sciences, Building 15, Tianjin University
> 
> No.92 Weijin Road, Nankai District, Tianjin 300072, China
> 
> 天津市南开区卫津路92号,天津大学生命科学学院15教学楼, 邮编:300072
> 
> 
> 
> 
> 
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Re: [ccp4bb] Phenix/refmac incompatibility?

[Robbie Joosten]

Hi Eleanor,This seems to be a caused by a bug in an older version of Phenix. We used to see quite a few examples of this on the PDB-REDO server, but not recently. Renumbering is the only solution I'm afraid.Cheers,RobbieOn 30 Dec 2021 20:05, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:I am not sure whether I have this straight but someone has sent a pdb file from phenix refinement with these atoms in the pdb file..ATOM   5580  N   GLY S  18      36.182  44.368  56.021  1.00 79.25           NATOM   5581  CA  GLY S  18      37.168  44.349  57.091  1.00 74.78           CATOM   5582  C   GLY S  18      37.048  43.211  58.097  1.00 73.20           CATOM   5583  O   GLY S  18      37.043  42.043  57.734  1.00 74.31           OATOM   5584  N   SER S  19      36.992  43.568  59.375  1.00 75.40           N...HETATM11068  O   HOH S  16      68.933  60.684 119.353  1.00 32.35           OHETATM11069  O   HOH S  17      17.772  20.649  91.306  1.00 40.79           OHETATM11070  O   HOH S  18      23.684  50.229  65.614  1.00 41.00           OHETATM11071  O   HOH S  19      45.488  71.114 105.890  1.00 51.50           OThen REFMAC gets upset because "residue" S 18 appears twice..Doesnt PHENIX worry about this? or has the user edits these HOH atoms into the file?And what should we do about itEleanor


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Re: [ccp4bb] Search for a particular motif [off-topic]

[Robbie Joosten]

You can analyse your hits with DSSP to see the secondary structure afterwards.Cheers,RobbieOn 19 Oct 2021 21:58, Guillaume Gaullier  wrote:
Hello,


ScanProsite almost does what you want, but since it only searches sequence databases, it has no notion of secondary structures and therefore cannot exclude motifs found in a secondary structure.
https://prosite.expasy.org/scanprosite/


I don’t know of any tool that would search structures and not only sequences. But if your motif isn’t too short or simple, ScanProsite should return a small enough number of hits that you could then inspect structures (or AlphaFold models) manually.


I hope this helps,












Guillaume















On 19 Oct 2021, at 20:43, Jan van Agthoven  wrote:



Dear all,
I apologize for the off-topic question. I’d like to search for a particular aa sequence motif inside the protein sequence data bank (Swiss-prot, Uniprot, etc…) with the following criteria:

It should not be inside a secondary structure.



Does anyone know a program that could do that?
Thanks,
Jan



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[ccp4bb] PDB-REDO downtime

[Robbie Joosten]

Dear BB-ers,

Due to electrical maintenance at our host institute pdb-redo.eu will be 
unavailable from 20:00h (Amsterdam) on October 15th to roughly 12:30h on 
October 16th. Apologies for the inconvenience.

Best wishes,
Robbie Joosten



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Re: [ccp4bb] PDB file secondary structure annotations

[Robbie Joosten]

Yes, you can use DSSP 4.0 (https://github.com/PDB-REDO/dssp) to directly 
annotate your structure model in PDB or mmCIF format. The latter is 
recommended. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Neno
> Vuksanovic
> Sent: Thursday, September 16, 2021 22:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] PDB file secondary structure annotations
> 
> Dear All,
> 
> I noticed that files available in the Protein Data Bank contain secondary
> structure information which allows for them to be imported in a program such
> as BioRender in order to make structural figures. However, the PDB files
> generated by PHENIX for structures that I haven't deposited yet do not contain
> such information so BioRender displays them as coils. Is there an easy way to
> add secondary structure information to a PDB file?
> 
> Best Regards,
> Neno
> 
> 
> 
> 
> 
> 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] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

[Robbie Joosten]

Hi everyone,

Thank you for the replies so far on and off list, they are really helpful. Feel 
free to keep them coming. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Dirk
> Kostrewa
> Sent: Tuesday, August 31, 2021 10:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset,
> pdbcur, coordconv, sftools
> 
> Dear Robbie,
> 
> I use pdbset in scripts from time to time, mainly to generate symmetry
> equivalent copies. I use sftools on the command line more frequently,
> because it allows a lot of mathematical operations on data in mtz files.
> I also use sftools to produce lists of average data values against
> resolution (that I plot then with gnuplot). I can't recall having used
> coordconv at all.
> 
> Best regards,
> 
> Dirk.
> 
> On 8/26/21 12:29 PM, Robbie Joosten wrote:
> > Dear CCP4 users,
> >
> > We (as in, the CCP4 developers) are investigating some (potentially)
> missing functionality in CCP4i2 and/or Cloud with respect to the programs
> pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old
> and may need to be replaced by other tools with similar functionality. Could
> you answer a few questions:
> >
> > - Do you use any of these tools?
> > - If so, how often? (Few times a week, month, year, or less than once a
> year).
> > - Which functionality of program X do you use?
> > - Would you like a graphical interface to that functionality or are you 
> > happy
> to use the command line?
> >
> > Personal example:
> > I use pdbset a few times a month, but only the "noise" function. I don't
> need a graphical interface for it (because it is used in the context of pdb-
> redo). I also use sftools, "reduce -> merge average" a few times a year. 
> Again,
> only from the command line.
> >
> >
> > Feel free to send your answers directly to me or to the bulletin board if
> you want to start a discussion. Tips on alternative CCP4 tools to achieve
> similar effects are probably also interesting for other BB users.
> >
> > Cheers,
> > Robbie
> >
> >
> >
> >
> >
> ###
> #
> >
> > 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
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> --
> 
> ***
> Dirk Kostrewa
> Gene Center Munich
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> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
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> Germany
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> ***
> 
> ###
> #
> 
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[ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

[Robbie Joosten]

Dear CCP4 users,

We (as in, the CCP4 developers) are investigating some (potentially) missing 
functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, 
pdbcur, coordconv, and sftools. Some of these tools are quite old and may need 
to be replaced by other tools with similar functionality. Could you answer a 
few questions:

- Do you use any of these tools? 
- If so, how often? (Few times a week, month, year, or less than once a year).
- Which functionality of program X do you use? 
- Would you like a graphical interface to that functionality or are you happy 
to use the command line?

Personal example:
I use pdbset a few times a month, but only the "noise" function. I don't need a 
graphical interface for it (because it is used in the context of pdb-redo). I 
also use sftools, "reduce -> merge average" a few times a year. Again, only 
from the command line.


Feel free to send your answers directly to me or to the bulletin board if you 
want to start a discussion. Tips on alternative CCP4 tools to achieve similar 
effects are probably also interesting for other BB users.

Cheers,
Robbie


 



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Re: [ccp4bb] AI papers in experimental macromolecular structure determination

[Robbie Joosten]

For model validation, this paper used machine learning (Random Forest) to 
detect peptide problems: https://doi.org/10.1107/S1399004715008263

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Bernhard
> Rupp
> Sent: Tuesday, August 3, 2021 22:00
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure
> determination
> 
> Maybe we should get to the root of this - what qualifies as machine learning
> and what not?
> 
> Do nonparametric predictors such as KDE qualify?
> 
> https://www.ruppweb.org/mattprob/default.html
> 
> Happy toa dd to the confusion.
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Tim
> Gruene
> Sent: Tuesday, August 3, 2021 11:59
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure
> determination
> 
> Hello Andrea,
> 
> profile fitting, like it is done in mosflm
> (https://doi.org/10.1107/S090744499900846X) or evalccd, or ... probably also
> qualify as AI/machine learning.
> 
> Best wishes,
> Tim
> 
> On Tue, 3 Aug 2021 11:43:06 +
> "Thorn, Dr. Andrea"  wrote:
> 
> > Dear colleagues,
> > I have compiled a list of papers that cover the application of
> > AI/machine learning methods in single-crystal structure determination
> > (mostly macromolecular crystallography) and single-particle Cryo-EM.
> > The draft list is attached below.
> >
> > If I missed any papers, please let me know. I will send the final list
> > back here, for the benefit of all who are interested in the topic.
> >
> > Best wishes,
> >
> >
> > Andrea.
> >
> >
> > __
> > General:
> > - Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B. &
> > Rosenberg, J. M. (2004). Acta Cryst D. 60, 1705–1716.
> > - Morris, R. J. (2004). Acta Cryst D. 60, 2133–2143.
> >
> > Micrograph preparation:
> > - (2020). Journal of Structural Biology. 210, 107498.
> >
> > Particle Picking:
> > - Sanchez-Garcia, R., Segura, J., Maluenda, D., Carazo, J. M. &
> > Sorzano, C. O. S. (2018). IUCrJ. 5, 854–865.
> > - Al-Azzawi, A., Ouadou, A., Tanner, J. J. & Cheng, J. (2019). BMC
> > Bioinformatics. 20, 1–26.
> > - George, B., Assaiya, A., Roy, R. J., Kembhavi, A., Chauhan, R.,
> > Paul, G., Kumar, J. & Philip, N. S. (2021). Commun Biol. 4, 1–12.
> > - Lata, K. R., Penczek, P. & Frank, J. (1995). Ultramicroscopy. 58,
> > 381–391.
> > - Nguyen, N. P., Ersoy, I., Gotberg, J., Bunyak, F. & White, T. A.
> > (2021). BMC Bioinformatics. 22, 1–28.
> > - Wang, F., Gong, H., Liu, G., Li, M., Yan, C., Xia, T., Li, X. &
> > Zeng, J. (2016). Journal of Structural Biology. 195, 325–336.
> > - Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004).
> > Journal of Structural Biology. 145, 157–167.
> >
> > Motion description in Cryo-EM:
> > - Matsumoto, S., Ishida, S., Araki, M., Kato, T., Terayama, K. &
> > Okuno, Y. (2021). Nat Mach Intell. 3, 153–160.
> > - Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. (2021). Nat
> > Methods. 18, 176–185.
> >
> > Local resolution:
> > - Avramov, T. K., Vyenielo, D., Gomez-Blanco, J., Adinarayanan, S.,
> > Vargas, J. & Si, D. (2019). Molecules. 24, 1181.
> > - Ramírez-Aportela, E., Mota, J., Conesa, P., Carazo, J. M. & Sorzano,
> > C. O. S. (2019). IUCrJ. 6, 1054–1063.
> > - (2021). QAEmap: A Novel Local Quality Assessment Method for Protein
> > Crystal Structures Using Machine Learning.
> >
> > Map post-processing:
> > - Sanchez-Garcia, R., Gomez-Blanco, J., Cuervo, A., Carazo, J. M.,
> > Sorzano, C. O. S. & Vargas, J. (2020). BioRxiv. 2020.06.12.148296.
> >
> > Secondary structure assignment in map:
> > - Subramaniya, S. R. M. V., Terashi, G. & Kihara, D. (2019). Nat
> > Methods. 16, 911–917.
> > - Li, R., Si, D., Zeng, T., Ji, S. & He, J. (2016). 2016 IEEE
> > International Conference on Bioinformatics and Biomedicine (BIBM),
> > Vol. pp. 41–46.
> > - Si, D., Ji, S., Nasr, K. A. & He, J. (2012). Biopolymers. 97,
> > 698–708.
> > - He, J. & Huang, S.-Y. Brief Bioinform.
> > - Lyu, Z., Wang, Z., Luo, F., Shuai, J. & Huang, Y. (2021). Frontiers
> > in Bioengineering and Biotechnology. 9,.
> > - Mostosi, P., Schindelin, H., Kollmannsberger, P. & Thorn, A.
> > (2020). Angewandte Chemie International Edition.
> >
> > Automatic structure building:
> > - Alnabati, E. & Kihara, D. (2020). Molecules. 25, 82.
> > - Si, D., Moritz, S. A., Pfab, J., Hou, J., Cao, R., Wang, L., Wu, T.
> > & Cheng, J. (2020). Sci Rep. 10, 1–22.
> > - Moritz, S. A., Pfab, J., Wu, T., Hou, J., Cheng, J., Cao, R., Wang,
> > L. & Si, D. (2019).
> > - Chojnowski, G., Pereira, J. & Lamzin, V. S. (2019). Acta Cryst D.
> > 75, 753–763.
> >
> > Crystallization:
> > - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64,
> > 1187–1195.
> > - (2004). Methods. 34, 390–407.
> > - Bruno, A. E., Charbonneau, P., Newman, J., Snell, E. H., So, D. R.,
> > Vanhoucke, V., Watkins, C. J., Williams, S. & Wilson, J. (2018). PLOS
> > ONE. 13, e0198883.
> >
> > Crystal centering:
> > - 

Re: [ccp4bb] pictures in emails

[Robbie Joosten]

Hear hear! On top of that, I look at my emails as plain text (so I can see 
where links go, much more secure). This means that I don't see that there is 
supposed to be a picture unless I convert the message back to HTML.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Edward
> Berry
> Sent: Sunday, July 18, 2021 17:17
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] pictures in emails
> 
> Two suggestions for people sending pictures of electron density to the BB:
> 
> 1. Reduce the size of the pictures-
> The two pictures in yesterday's email appear nice and small in my email
> client, but still illustrate what is being described. However they are 
> actually
> 4032x3024 and 2040x1458 pixels, making for rather large emails. All that
> extra resolution is wasted unless the user opens the image directly ("view
> image"), and in any case is completely unnecessary for the point being made.
> I think about 600x600 pixels is plenty for almost anything you want to show
> in electron density.
> This does not require manipulation in photoshop or such- just reduce the
> size of the graphics window and take a screenshot of that window.
> 
> 2. send the picture as an attachment rather than inline. That way it won't be
> included in all the replies. Or if the people replying could find some way to
> exclude pictures or formt the reply as plain-text, that would help.
> 
> (No, I'm not receiving these emails via 1200 baud modem- but I like to save
> the messages for future reference. If the trend continues toward high-
> resolution inline screenshots, that will take a significant amount of disk
> space. And yes, I know there is an archive.)
> eab
> 
> ###
> #
> 
> 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] PDB-REDO question

[Robbie Joosten]

Hi Joern,

Yes, these values are all stored in a file called data.json that each entry 
has. The keys that are most relevant are:
BLTBEST (geometric restraint weight)
BBEST (B-factor restraint weight)
BREFTYPE (B-factor model)
DOTLS (Whether or not TLS refinement is used)
ISTWIN (Whether or not the data are perceived as twinned)
RSHRINK (Solvent mask shrinkage)
VDWPROBE (Solvent mask probe)
IONPROBE (Solvent mask ion probe)

Feel free, to ask what the other keys mean. Most of them are model statistics, 
there are a lot of them.

HTH,
Robbie



> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Joern
> Krausze
> Sent: Friday, May 28, 2021 10:26
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] PDB-REDO question
> 
>   Dear all,
> 
> 
> I want to do the following: I want to download several structures from
> PDB-REDO and pipe them into Refmac5 for re-refinement, replacing the
> restraints dictionary of a certain ligand with a customized one. The
> refinement settings I want to keep otherwise unchanged. We are talking
> about a few hundred structures here, so I prefer to do this via a shell
> script.
> 
> Are the Refmac5 settings that PDB-REDO used for redoing the deposited
> structures to be found somewhere? For my own structures, I get a
> *.refmac file that I can directly pipe into Refmac5. However, I didn't
> find such a file for the deposited structures. Is there a way to get my
> hands on it?
> 
> 
> Thanks in advance & best wishes,
> 
> Joern
> 
> --
> *
> Address:
> 
> Joern Krausze
> Braunschweig University of Technology
> Institute of Plant Biology
> Spielmannstr. 7
> 38106 Braunschweig
> Germany
> 
> Email:  j.krau...@tu-braunschweig.de
> Phone:  +49 (0)531 3915858
> *
> 
> ###
> #
> 
> 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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[ccp4bb] PDB-REDO downtime

[Robbie Joosten]

Dear CCP4bb-ers,

The server room that hosts the PDB-REDO infrastructure will be getting a new 
air conditioner soon. This means that PDB-REDO will be unavailable from 20:00h 
(CET) on April 18th until the same time on the 19th (give or take). After that 
PDB-REDO will be available again, cooler than ever.

All the best,
Robbie



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Re: [ccp4bb] coot & other graphics programs draw too many bonds

[Robbie Joosten]

Hi Fred,

I think this is a problem of not having the right description of the compound. 
Have you tried using a restraint file for the compound in Coot so the bonds are 
properly defined? Note sure if Coot uses them, but perhaps also remove all the 
CONECT records.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Fred
> Vellieux
> Sent: Thursday, April 1, 2021 15:02
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] coot & other graphics programs draw too many bonds
> 
> Hello there,
> 
> After running autodock vina on certain small molecules, the graphics
> software I am using (e.g. Pymol, Coot) draws far too many bonds on the
> docked small molecule. See enclosed screen capture.
> 
> Is there any way to prevent this from happening? This isn't very satisfactory
> of you wish to produce figures for a presentation or for publication.
> 
> Ta,
> 
> Fred.
> 
> --
> MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech
> Republic
> 
> 
> ###
> #
> 
> 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] poly-dN model

[Robbie Joosten]

Hi Reza,

The equivalent for UNK (not ALA!) is residue N for RNA and DN for DNA.

HTH,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Reza
> Khayat
> Sent: Saturday, March 13, 2021 14:53
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] poly-dN model
> 
> Hi,
> 
> 
> 
> 
> 
> For DNA/RNA models, is there an equivalent to a poly-Ala model? Something
> like a poly-dN perhaps? This is in case you don't know the nucleic acid
> sequence. Thanks.
> 
> 
> 
> 
> 
> Best wishes,
> Reza
> 
> 
> 
> 
> 
> Reza Khayat, PhD
> Associate Professor
> City College of New York
> Department of Chemistry and Biochemistry New York, NY 10031
> 
> 
> 
> 
> 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] Linux Distro for setting up workstations - Is CentOS still a good choice?

[Robbie Joosten]

Big fan of Ubuntu here. The Long Term Support versions work very well and 
everything you need is on them. At the same time Debian tends to be less 
conservative that the Red Had universe which typically makes it easier to get 
modern things running. Also the Ubuntu on WSL (Windows) is a lifesaver and is 
really easy to use.

We are bringing more and more of our software the Debian repository. It makes 
it much easier to deploy. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Tim
> Gruene
> Sent: Saturday, February 20, 2021 16:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS 
> still
> a good choice?
> 
> Hi Matthias,
> 
> I have been using Debian for more than a decade. Every stable release is
> supported for at least 5 years.
> Many crystallographic libraries and some programs are part of the standard
> repository, like raster3d, pymol, shelxle, libccp4, libclipper, ...
> 
> Debian is particularly stable, and requires little maintenance.
> 
> Cheers,
> Tim
> 
> On Fri, 19 Feb 2021 21:35:46 +0100
> Matthias Zeug  wrote:
> 
> > Hi all,
> >
> >
> >
> > I just came across the (already quite old) news that Red-Hat switches
> > their support-policy for CentOS to a rolling preview model (replacing
> > CentOS Linux by CentOS Stream):
> >
> > https://www.zdnet.com/article/why-red-hat-dumped-centos-for-centos-
> str
> > eam/
> >
> > https://www.enterpriseai.news/2021/01/22/red-hats-disruption-of-centos
> > -unlea
> > shes-storm-of-dissent/
> >
> >
> >
> > I wondered if that has any implications for the community, as
> > scientific programs - maybe except the big ones like coot, Phenix, and
> > ccp4 - are often not *that* well maintained for an extended period. I
> > had the impression CentOS was liked especially for its
> > "unbreakability,"  and it seems to be the main developing platform for
> > some widely used smaller programs (e.g., adxv).
> >
> >
> >
> > Do you think it would be advisable to switch to a Ubuntu-distro when
> > setting up new workstations in the future, or is it safe to stick to
> > CentOS?
> >
> >
> >
> > Please let me know what you think :-)
> >
> >
> >
> > Best,
> >
> >
> >
> > Matthias
> >
> >
> >
> >
> >
> > Matthias Zeug
> >
> > Buchmann Institute of Molecular Life Sciences
> >
> > Goethe University Frankfurt
> >
> >
> >
> >
> >
> ###
> ###
> > ##
> >
> > 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/
> 
> 
> 
> --
> --
> 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
> 
> ###
> #
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
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Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

[Robbie Joosten]

Hi Tim,

Very good points. The big picture is hard to grasp and we end up taking 
political choices rather than anything else. I'm very glad that we can 
outsource these choices to others every four year here.

Lockdowns may save lives in the here and now, but the global economic damage 
makes life for others much harder to a point that it may actually kill them. 
Economic decline in the First World may be something with which that we can 
deal but, like viruses, it blows over to other parts of the world where 
economic growth is the real life saver. Does the prolonging of a reasonably 
measurable number well-lived lives in the West outweigh the extinguishing of a 
hard-to-assess number of much younger lives in the rest of the world? I'm glad 
I don't have to make that call.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Tim
> Gruene
> Sent: Friday, February 19, 2021 09:33
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"
> 
> Hi Jessica,
> 
> one comment: death cannot be prevented. It is a certainty as soon as you
> are born (well, 9 months before).
> 
> While this seems an obvious subtlety, many of the current measures seems
> to be influenced by the (probably unconscious) belief one can defeat death.
> We can only reduce the risk to die at a certain moment and of a certain
> cause.
> 
> The example of rabbits in Australia also illustrates how simple minded
> humans generally are: we focus on one thing, but usually fail to take a larger
> picture into account.
> 
> Cheers,
> Tim
> 
> 
> 
> On Thu, 18 Feb 2021 08:16:59 -0800 Jessica Bruhn
>  wrote:
> 
> > Hello,
> >
> > There have been some really excellent points raised by others
> > (informed consent, feasibility, etc), but I would like to share a
> > story about another time humans tried to release a virus on a wild
> > population in order to further an arguably noble goal:
> >
> > In the 1850s European rabbits were introduced in Australia for sport
> > hunting. They quickly did what bunnies do and started to become a real
> > problem. In the 1950s, scientists decided to introduce myxoma virus to
> > Australia, which is 90-99% fatal for European rabbits, but less lethal
> > for the native rabbits. They intentionally released this virus and in
> > the first year the mortality rate was 99.8% for the European rabbits.
> > Yay, right??? Unfortunately, in the subsequent year the mortality rate
> > fell to 25% and steadily continued to fall until it was lower than the
> > reproductive rate of the European rabbits. The host-virus interaction
> > played itself out: less-virulent viruses arose and resistant rabbits
> > were selected for.
> >
> > To me it seems unwise to assume a replication competent virus
> > (engineered or not) would refrain from mutating and adapting upon
> > release, especially over the time course that would be required to
> > infect all 7 billion+ humans on this planet. To me, I feel our options
> > are (1) reach herd immunity through natural infection and accept the
> > preventable deaths of many millions of people or (2) continue with
> > non-pharmaceutical interventions (mask wearing, distancing, etc) until
> > we can vaccinate enough people to reach herd immunity and hopefully by
> > that time we have robust testing and treatment options available for
> > those who continue to fall ill after we reach herd immunity. We as
> > humans did something amazing by producing multiple safe and effective
> > vaccines in less than one year, and I would like us to continue trying
> > to save as many lives as possible by employing these vaccines as
> > widely as possible.
> >
> > Anyways, take care. I know the pandemic is hard on all of us.
> >
> > Best regards,
> > Jessica
> >
> > On Thu, Feb 18, 2021 at 6:15 AM Patrick Shaw Stewart
> >  wrote:
> >
> > > I agree with those who say that A and B are usually incompatible.
> > >
> > > If we're like
> > > chickens-in-a-barn-that-have-been-infected-with-bird-flu, the virus
> > > very rapidly becomes more virulent (hospital and care-home
> > > infections?).  It's hard for a virus to infect your nose and throat
> > > quickly, and then stop.
> > >
> > > In the medium term the herd will build up some immunity and then
> > > we'll become more like wandering albatrosses: the virus has to keep
> > > us on the move if it's going to get itself near another susceptible
> > > host.
> > >
> > > IMO the way a *respiratory *virus tries to "have its cake and eat
> > > it" - that is, get as much of both A and B as possible - is to
> > > develop thermal sensitivity.  I.e. infect nose and throat but keep
> > > out of lungs and brain :
> > >
> > > https://www.preprints.org/manuscript/202101.0389/v1
> > >
> > >
> > >
> > > Thanks, Patrick
> > >
> > >
> > > On Wed, Feb 17, 2021 at 9:46 PM Edwin Pozharski
> > >  wrote:
> > >
> > >> I guess for such vehicle to be "extremely contagious" (or
> > >> contagious at all for that matter) it should 

Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO

[Robbie Joosten]

All the (library) code is open source with a BSD license, so yes this is 
possible.

Cheers,
Robbie

> -Original Message-
> From: Boaz Shaanan 
> Sent: Monday, January 18, 2021 22:57
> To: Robbie Joosten 
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO
> 
> Hi,
> Will it be possible to include the rama-z analysis in Coot (perhaps as a
> plugin)?
> Boaz
> 
> Boaz Shaanan, Ph.D.
> Department of Life Sciences
> Ben Gurion University of the Negev
> Beer Sheva
> Israel
> 
> On Jan 18, 2021 22:47, Robbie Joosten 
> wrote:
> 
> Dear all,
> 
> During the last CCP4 meeting, Oleg presented our collaboration with the
> Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then,
> some asked for a convenient way to get this score. You are now welcome to
> use: https://pdb-redo.eu/tortoize
> 
> This is a quick and easy way to check you model. Just upload your structure
> model (and restraints if you have non-standard compounds) and press
> "calculate". You get the Ramachandran Z-score with an error margin and you
> get the side-chain equivalent (also known as the Chi-1/Chi-2 Z-score in
> WHAT_CHECK) for free.
> 
> There are two more ways to get the score, that might be relevant for
> specialized use:
> 1) use the webservice to get the same values and the per-residue values in
> an easy-to-parse JSON file. For example through curl with the command: curl
> -F data=@1cbs_final.pdb -F dict=@/zata/ccp4-
> 7.1/lib/data/monomers/a/ALA.cif  https://pdb-redo.eu/tortoize. Note that
> the "dict" value is optional. Any other POST on https://pdb-redo.eu/tortoize
> would also work.
> 
> 2) to analyse a very large group of models you are encouraged to install
> tortoize locally. It's available on https://github.com/PDB-REDO/tortoize with
> a BSD license.
> 
> The scores are also of course available after each PDB-REDO run: the Rama-Z
> is one of the model quality metrics. All  methods take PDB and mmCIF
> formatted files as longs as they are valid, i.e. fit the current format
> specification (mmCIF) or contain at least a CRYST1 record (PDB). As always,
> constructive feedback is appreciated.
> 
> If you use Rama-Z, please do cite:
> Sobolev et al. A Global Ramachandran Score Identifies Protein Structures
> with Unlikely Stereochemistry; Structure;
> https://doi.org/10.1016/j.str.2020.08.005
> 
> All the best on behalf of Team REDO,
> Robbie
> 
> ###
> #
> 
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO

[Robbie Joosten]

Dear all,

During the last CCP4 meeting, Oleg presented our collaboration with the Phenix 
team, about the Ramachandran plot Z-score (or Rama-Z). Since then, some asked 
for a convenient way to get this score. You are now welcome to use: 
https://pdb-redo.eu/tortoize

This is a quick and easy way to check you model. Just upload your structure 
model (and restraints if you have non-standard compounds) and press 
"calculate". You get the Ramachandran Z-score with an error margin and you get 
the side-chain equivalent (also known as the Chi-1/Chi-2 Z-score in WHAT_CHECK) 
for free. 

There are two more ways to get the score, that might be relevant for 
specialized use:
1) use the webservice to get the same values and the per-residue values in an 
easy-to-parse JSON file. For example through curl with the command: curl -F 
data=@1cbs_final.pdb -F dict=@/zata/ccp4-7.1/lib/data/monomers/a/ALA.cif  
https://pdb-redo.eu/tortoize. Note that the "dict" value is optional. Any other 
POST on https://pdb-redo.eu/tortoize would also work.

2) to analyse a very large group of models you are encouraged to install 
tortoize locally. It's available on https://github.com/PDB-REDO/tortoize with a 
BSD license. 

The scores are also of course available after each PDB-REDO run: the Rama-Z is 
one of the model quality metrics. All  methods take PDB and mmCIF formatted 
files as longs as they are valid, i.e. fit the current format specification 
(mmCIF) or contain at least a CRYST1 record (PDB). As always, constructive 
feedback is appreciated. 

If you use Rama-Z, please do cite: 
Sobolev et al. A Global Ramachandran Score Identifies Protein Structures with 
Unlikely Stereochemistry; Structure;  https://doi.org/10.1016/j.str.2020.08.005

All the best on behalf of Team REDO, 
Robbie



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Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Robbie Joosten]

Dear Jasmine,

I have a few questions about this bit:
//
As some users pointed out, single NAG could be just a part of the glycan that 
the author chose to build, as most natural N-glycans must have stem of a common 
core of 5 monosaccharides or its fucosylated version, such as those modeled in 
the PDB ID 6WPS. However, the PDB is a 3D-atomic coordinate archive in which 
the model coordinates are built based on supporting experimental data. 
Therefore, carbohydrates are described as-is in the modeled structures without 
reference to missing components of the presumed oligosaccharide sequence. If 
the author only builds a monosaccharide, then this monosaccharide is described 
as a non-polymer ligand.
//
Is it technically allowed to have a single, covalently bound carbohydrate 
described as a branched entity of length 1?
If so, if an author does specify such a single modeled residue as branched 
entity, for instance because (s)he has a good reason to suspect that a second 
residue was there, but isn’t comfortable with building it, then is this 
specification kept in annotation?
If not, do you expect model building programs to switch from branched to 
non-poly entities when a second residue is removed when a model is written out? 
And back again when a residue is added? I find this rather unpractical from an 
implementation point of view. We change carbohydrate trees quite regularly.

Cheers,
Robbie


From: CCP4 bulletin board  On Behalf Of Jasmine Young
Sent: Tuesday, December 8, 2020 21:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- 
N-glycans are now separate chains if more than one residue

Dear PDB Data Users:

Thank you for providing feedback on the results of an archival-level 
carbohydrate remediation project that led to the re-release of over 14,000 PDB 
structures in July 2020. This update includes diverse oligosaccharides: 
glycosylation; metabolites such as maltose, sucrose, cellulose fragments; 
glycosaminoglycans, such as fragments of heparin and heparan sulfate; epitope 
patterns such as A/B blood group antigens and the H-type or Lewis-type stems; 
and many artificial carbohydrates mimicking or counting natural products 
(https://www.wwpdb.org/documentation/carbohydrate-remediation).

Starting in 2017, this PDB remediation aimed to standardize the biochemical 
nomenclature of the carbohydrate components following the IUPAC-IUBMB 
recommendations established by the carbohydrate community 
(https://media.iupac.org/publications/pac/1996/pdf/6810x1919.pdf), and to 
provide uniform representation of oligosaccharides to improve the 
identification and searchability of oligosaccharides modeled in the PDB 
structures.  During the remediation planning, wwPDB consulted community users 
and the PDBx/mmCIF Working Group and made data files available on GitHub in 
early 2020 for community feedback. wwPDB has collaborated with Robert Woods at 
University of Georgia in US, researchers at The Noguchi Institute and Soka 
University in Japan, and Thomas Lutteke in Germany to generate uniform linear 
descriptors for the oligosaccharide sequences.

To achieve these community goals, each oligosaccharide is represented as a 
branched entity with complete biochemical description and each glycosidic 
linkage specified. The full representation of carbohydrates is provided in the 
mmCIF format file, but this is not possible in legacy PDB format files (as the 
format has been frozen since 2012 
(https://www.wwpdb.org/documentation/file-formats-and-the-pdb).

Proper indexing is necessary for branched entity representation and for 
generation of linear descriptors, hence the ordering (numbering) starts at the 
reducing end (#1), where the glycosylation occurs, to the non-reducing end in 
ascending order. Unique chain IDs are assigned to branched entities 
(oligosaccharides) to avoid residue numbering overlapped with protein residues 
and to enable consistent numbering for every oligosaccharide. For example, in 
PDB ID 6WPS, there are 5 oligosaccharides associated with the same protein 
chain A, the consistent ordering and numbering can only be retained with unique 
chain ID for each oligosaccharide in both PDBx/mmCIF and PDB format files

For archival consistency, a single-monosaccharide is defined as a non-polymer 
and treated consistently with other non-polymer ligands in the PDB. A 
single-monosaccharide occurring at a glycosylation site has a unique chain ID 
in the PDBx/mmCIF file (_atom_site.label_asym_id) but not in the PDB format 
file.

Using PDB ID 6WPS as an example, the PDBx/mmCIF data item 
_atom_site.label_asym_id corresponds to the column #7 in the atom_site 
coordinates section has an asym ID ‘Y’ for the 1st instance of 
single-monosaccharide, NAG bound to ASN 61 of protein chain ‘A’. The ‘Y’ value 
is unique for this monosaccharide. The additional chain ID 
(_atom_site.auth_asym_id) in the PDBx/mmCIF file that mapped to the PDB format 
file for 

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Robbie Joosten]

[ccp4bb] Coming July 29: Improved Carbohydrate Data at
> > the PDB -- N-glycans are now separate chains if more than one residue
> >
> >      This suggestion violates a basic principle of data base theory.
> > A single data item cannot encode two pieces of information.  The whole
> > structure of CIF falls apart if this is done.
> >
> >      Does the new PDB convention contain a CIF record of the link that
> > bridges between the protein chain and the, now separated, glycan chain?
> >    If not, I think this is the principle failing of their new scheme.
> >
> > Dale Tronrud
> >
> > On 12/4/2020 12:06 AM, Tristan Croll wrote:
> >> To go one step further: in large, heavily glycosylated multi-chain
> >> complexes the assignment of a random new chain ID to each glycan will
> >> lead to headaches for people building visualisations using existing
> >> viewers, because it loses the easy name-based association  of glycan
> >> to parent protein chain. A suggestion: why not take full
> > advantage of the mmCIF capability for multi-character chain IDs, and
> > name them by appending characters to the parent chain ID? Using chain
> > A as an example, perhaps the glycans could become Ag1, Ag2, etc.?
> >>
> >>> On 4 Dec 2020, at 07:48, Luca Jovine  wrote:
> >>>
> >>> CC: pdb-l
> >>>
> >>> Dear Zhijie and Robbie,
> >>>
> >>> I agree with both of you that the new carbohydrate chain assignment
> convention that has been recently adopted by PDB introduces confusion,
> not just for PDB-REDO but also - and especially - for end users.
> >>>
> >>> Could we kindly ask PDB to improve consistency by either assigning a
> >>> separate chain to all covalently attached carbohydrates (regardless
> >>> of whether one or more residues have been traced), or reverting to
> >>> the old system (where N-/O-glycans inherited the same  chain ID of
> >>> the protein to which they are attached)? The current
> > hybrid solution hardly seems optimal...
> >>>
> >>> Best regards,
> >>>
> >>> Luca
> >>>
> >>>> On 3 Dec 2020, at 20:17, Robbie Joosten
>  wrote:
> >>>>
> >>>> Dear Zhijie,
> >>>>
> >>>> In generally I like the treatment of carbohydrates now as branched
> polymers. I didn't realise there was an exception. It makes sense for unlinked
> carbohydrate ligands, but not for N- or O-glycosylation sites as these might
> change during model building or,  in my case, carbohydrate rebuilding in
> PDB-REDO powered by Coot.
> > Thanks for pointing this out.
> >>>>
> >>>> Cheers,
> >>>> Robbie
> >>>>
> >>>>> -Original Message-
> >>>>> From: CCP4 bulletin board  On Behalf Of
> >>>>> Zhijie Li
> >>>>> Sent: Thursday, December 3, 2020 19:52
> >>>>> To: CCP4BB@JISCMAIL.AC.UK
> >>>>> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data
> >>>>> at the PDB -- N-glycans are now separate chains if more than one
> >>>>> residue
> >>>>>
> >>>>> Hi all,
> >>>>>
> >>>>> I was confused when I saw mysterious new glycan chains emerging
> >>>>> during PDB deposition and spent quite some time trying to find out
> >>>>> what was wrong with my coordinates.  Then it occurred to me that a
> >>>>> lot of recent structures also had tens of N-glycan chains.
> >>>>> Finally I realized that this phenomenon is a consequence of this PDB
> policy announced here in July.
> >>>>>
> >>>>>
> >>>>> For future depositors who might also get puzzled, let's put it in
> >>>>> a short
> >>>>> sentence:  O- and N-glycans are now separate chains if it they
> >>>>> contain more than one residue; single residues remain with the
> protein chain.
> >>>>>
> >>>>>
> >>>>>
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2F
> >>>>> www.wwpdb.org%2Fdocumentation%2Fcarbohydrate-
> remediationdata=
> >>>>>
> 04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47
> %7
> >>>>>
> Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065%
> 7CU
> >>>>>
> nknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLC

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Robbie Joosten]

Hi Luca,

Your point remains completely valid and I agree that residues that can belong 
to a longer chain should be treated as such. The same problem is with peptide 
ligands (at least in PDB times), if they consist of three residues they would 
their own chains, with 2 residues they would not. It's spectacular how much 
code beaks on that. 

At the same time you have to understand that the PDB makes design choices and 
that some experimentalist will find an exception. Yes, there are PDB entries 
where they add amino acids as crystallisation additives. As an interesting 
exception, this works better for nucleic acids: A loose nucleotide, say AMP, 
has a different name than a nucleotide that is part of a polymer. 

Anyway, we should appreciate the work that goes into setting up something as 
the PDB which is, by all means, a triumph in biological databases and an 
example to other fields.

Cheers,
Robbie



> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Luca
> Jovine
> Sent: Friday, December 4, 2020 18:45
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
> PDB -- N-glycans are now separate chains if more than one residue
> 
> Dear Dale and Robbie,
> 
> I agree with your comments! But may I stir back the discussion to the
> original issue, which is that one-residue N-glycans are now treated
> differently from multi-residue N-glycans (although they are both covalently
> linked to a protein chain)? This inconsistency is independent of the file
> format…
> 
> Best, Luca
> 
> 
>   On 4 Dec 2020, at 18:30, Robbie Joosten
> mailto:robbie_joos...@hotmail.com>
> > wrote:
> 
>   Dear Dale,
> 
>   Yes, good point. Let's stop bending over backwards to come up with
> faux PDB compatibility and focus on making mmCIF better.
> 
>   There are struct_conn records that describe the linkages. This is
> enough to reconstruct the connectivity. There is an ongoing debate on how
> to capture the restraints for such linkages. But at least this can in 
> principle be
> captured in mmCIF whereas this is pretty much undoable in PDB format.
> 
>   Cheers,
>   Robbie
> 
> 
>   On 4 Dec 2020 18:01, Dale Tronrud  <mailto:de...@daletronrud.com> > wrote:
> 
> 
> 
>   This suggestion violates a basic principle of data base
> theory.  A
>   single data item cannot encode two pieces of information.
> The whole
>   structure of CIF falls apart if this is done.
> 
>   Does the new PDB convention contain a CIF record of the
> link that
>   bridges between the protein chain and the, now separated,
> glycan chain?
> If not, I think this is the principle failing of their new
> scheme.
> 
>   Dale Tronrud
> 
>   On 12/4/2020 12:06 AM, Tristan Croll wrote:
>   > To go one step further: in large, heavily glycosylated multi-
> chain complexes the assignment of a random new chain ID to each glycan
> will lead to headaches for people building visualisations using existing
> viewers, because it loses the easy name-based association of glycan to
> parent protein chain. A suggestion: why not take full advantage of the
> mmCIF capability for multi-character chain IDs, and name them by
> appending characters to the parent chain ID? Using chain A as an example,
> perhaps the glycans could become Ag1, Ag2, etc.?
>   >
>   >> On 4 Dec 2020, at 07:48, Luca Jovine  <mailto:luca.jov...@ki.se> > wrote:
>   >>
>   >> CC: pdb-l
>   >>
>   >> Dear Zhijie and Robbie,
>   >>
>   >> I agree with both of you that the new carbohydrate chain
> assignment convention that has been recently adopted by PDB introduces
> confusion, not just for PDB-REDO but also - and especially - for end users.
>   >>
>   >> Could we kindly ask PDB to improve consistency by either
> assigning a separate chain to all covalently attached carbohydrates
> (regardless of whether one or more residues have been traced), or reverting
> to the old system (where N-/O-glycans inherited the same chain ID of the
> protein to which they are attached)? The current hybrid solution hardly
> seems optimal...
>   >>
>   >> Best regards,
>   >>
>   >> Luca
>   >>
>   >>> On 3 Dec 2020, at 20:17, Robbie Joosten
> mailto:robbie_joos...@hotmail.com>
> > wrote:
>   >>>
>

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Robbie Joosten]

Dear Dale,Yes, good point. Let's stop bending over backwards to come up with faux PDB compatibility and focus on making mmCIF better.There are struct_conn records that describe the linkages. This is enough to reconstruct the connectivity. There is an ongoing debate on how to capture the restraints for such linkages. But at least this can in principle be captured in mmCIF whereas this is pretty much undoable in PDB format.Cheers,RobbieOn 4 Dec 2020 18:01, Dale Tronrud  wrote:

    This suggestion violates a basic principle of data base theory.  A 

single data item cannot encode two pieces of information.  The whole 

structure of CIF falls apart if this is done.



    Does the new PDB convention contain a CIF record of the link that 

bridges between the protein chain and the, now separated, glycan chain? 

  If not, I think this is the principle failing of their new scheme.



Dale Tronrud



On 12/4/2020 12:06 AM, Tristan Croll wrote:

> To go one step further: in large, heavily glycosylated multi-chain complexes the assignment of a random new chain ID to each glycan will lead to headaches for people building visualisations using existing viewers, because it loses the easy name-based association of glycan to parent protein chain. A suggestion: why not take full advantage of the mmCIF capability for multi-character chain IDs, and name them by appending characters to the parent chain ID? Using chain A as an example, perhaps the glycans could become Ag1, Ag2, etc.?

> 

>> On 4 Dec 2020, at 07:48, Luca Jovine  wrote:

>>

>> CC: pdb-l

>>

>> Dear Zhijie and Robbie,

>>

>> I agree with both of you that the new carbohydrate chain assignment convention that has been recently adopted by PDB introduces confusion, not just for PDB-REDO but also - and especially - for end users.

>>

>> Could we kindly ask PDB to improve consistency by either assigning a separate chain to all covalently attached carbohydrates (regardless of whether one or more residues have been traced), or reverting to the old system (where N-/O-glycans inherited the same chain ID of the protein to which they are attached)? The current hybrid solution hardly seems optimal...

>>

>> Best regards,

>>

>> Luca

>>

>>> On 3 Dec 2020, at 20:17, Robbie Joosten  wrote:

>>>

>>> Dear Zhijie,

>>>

>>> In generally I like the treatment of carbohydrates now as branched polymers. I didn't realise there was an exception. It makes sense for unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as these might change during model building or, in my case, carbohydrate rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.

>>>

>>> Cheers,

>>> Robbie

>>>

>>>> -Original Message-

>>>> From: CCP4 bulletin board  On Behalf Of Zhijie Li

>>>> Sent: Thursday, December 3, 2020 19:52

>>>> To: CCP4BB@JISCMAIL.AC.UK

>>>> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the

>>>> PDB -- N-glycans are now separate chains if more than one residue

>>>>

>>>> Hi all,

>>>>

>>>> I was confused when I saw mysterious new glycan chains emerging during

>>>> PDB deposition and spent quite some time trying to find out what was

>>>> wrong with my coordinates.  Then it occurred to me that a lot of recent

>>>> structures also had tens of N-glycan chains.  Finally I realized that this

>>>> phenomenon is a consequence of this PDB policy announced here in July.

>>>>

>>>>

>>>> For future depositors who might also get puzzled, let's put it in a short

>>>> sentence:  O- and N-glycans are now separate chains if it they contain more

>>>> than one residue; single residues remain with the protein chain.

>>>>

>>>>

>>>> https://eur01.safelinks.protection.outlook.com/?url=""

>>>>

>>>> "Oligosaccharide molecules are classified as a new entity type, branched,

>>>> assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF

>>>> category introduced to define the type of branching

>>>> (_pdbx_entity_branch.type) . "

>>>>

>>>>

>>>>

>>>>

>>>>

>>>> I found the differential treatment of single-residue glycans and multi-residue

>>>> glycans not only bit lack of aesthetics but also misleading.  When a structure

>>>> contains both NAG-NAG... and single NAG on N-glycosylation sites, it might

>>>> be because of lack of density for building more residues, or because that

>>>> som

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Robbie Joosten]

Dear Zhijie,

In generally I like the treatment of carbohydrates now as branched polymers. I 
didn't realise there was an exception. It makes sense for unlinked carbohydrate 
ligands, but not for N- or O-glycosylation sites as these might change during 
model building or, in my case, carbohydrate rebuilding in PDB-REDO powered by 
Coot. Thanks for pointing this out.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Zhijie Li
> Sent: Thursday, December 3, 2020 19:52
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
> PDB -- N-glycans are now separate chains if more than one residue
> 
> Hi all,
> 
> I was confused when I saw mysterious new glycan chains emerging during
> PDB deposition and spent quite some time trying to find out what was
> wrong with my coordinates.  Then it occurred to me that a lot of recent
> structures also had tens of N-glycan chains.  Finally I realized that this
> phenomenon is a consequence of this PDB policy announced here in July.
> 
> 
> For future depositors who might also get puzzled, let's put it in a short
> sentence:  O- and N-glycans are now separate chains if it they contain more
> than one residue; single residues remain with the protein chain.
> 
> 
> https://www.wwpdb.org/documentation/carbohydrate-remediation
> 
> "Oligosaccharide molecules are classified as a new entity type, branched,
> assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF
> category introduced to define the type of branching
> (_pdbx_entity_branch.type) . "
> 
> 
> 
> 
> 
> I found the differential treatment of single-residue glycans and multi-residue
> glycans not only bit lack of aesthetics but also misleading.  When a structure
> contains both NAG-NAG... and single NAG on N-glycosylation sites, it might
> be because of lack of density for building more residues, or because that
> some of the glycosylation sites are now indeed single NAGs (endoH etc.)
> while some others are not cleaved due to accessibility issues.Leaving NAGs
> on the protein chain while assigning NAG-NAG... to a new chain, feels like
> suggesting something about their true oligomeric state.
> 
> 
> For example, for cryoEM structures, when one only builds a single NAG at a
> site does not necessarily mean that the protein was treated by endoH. In
> fact all sites are extended to at least tri-Man in most cases. Then why
> keeping some sites associated with the protein chain while others kicked
> out?
> 
> Zhijie
> 
> 
> 
> 
> 
> From: CCP4 bulletin board  on behalf of John
> Berrisford 
> Sent: Thursday, July 9, 2020 4:39 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB
> 
> 
> Dear CCP4BB
> 
> PDB data will shortly incorporate a new data representation for
> carbohydrates in PDB entries and reference data that improves the
> Findability and Interoperability of these molecules in macromolecular
> structures. In order to remediate and improve the representation of
> carbohydrates across the archive, the wwPDB has:
> 
> * standardized Chemical Component Dictionary nomenclature
> following IUPAC-IUBMB recommendations
> * provided uniform representation for oligosaccharides
> * adopted Glycoscience-community commonly used linear descriptors
> using community tools
> * annotated glycosylation sites in PDB structures
> 
> Starting July 29, 2020, users will be able to access the improved data via FTP
> or wwPDB partner websites. Detailed information about this project is
> available at the wwPDB website
>  ; lists
> of impacted entries and chemical components will be published on this page
> after data release.
> 
> The wwPDB has created a new ‘branched’ entity representation for
> polysaccharides, describing all the individual monosaccharide components of
> these in the PDB entry. As part of this process, we have standardized atom
> nomenclature of >1,000 monosaccharides in the Chemical Component
> Dictionary (CCD) and applied a branched entity representation to
> oligosaccharides for >8000 PDB entries. To guarantee unambiguous chemical
> description of oligosaccharides in the affected PDB entries, an explicit
> description of covalent linkage information between their monosaccharide
> units is included. In addition, wwPDB validation reports provide consistent
> representation for these oligosaccharides and include 2D representations
> based on the Symbol Nomenclature for Glycans (SNFG).
> 
> To support the remediation of carbohydrate representation, software tools
> providing linear descriptors were developed in collaboration with the
> glycoscience community to enable easy translation of PDB data to other
> representations commonly used by glycobiologists. These include Condense
> IUPAC from GMML   at University
> of Georgia, 

Re: [ccp4bb] Refmac not handling microheterogeneity?

[Robbie Joosten]

Hi Ian,

AFAIK there is no clean solution for this and I imagine this problem goes very 
deep into the internal representation of the model in REFMAC. That said, 1 in 6 
missing PDB-REDO entries is caused by this problem, so a solution would be very 
welcome.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ian
> Tickle
> Sent: Wednesday, December 2, 2020 15:02
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac not handling microheterogeneity?
> 
> 
> Dear All
> 
> I just downloaded a PDB file (7A5V) from the EBI server, tried to run Refmac
> on it and got the error:
> 
> ERROR: in chain A residue: 279 different residues have the same number
> There is an error in the input coordinate file
> 
> At least one the chains has 2 residues with the same number ===> Error:
> Problem with coordinate file
> 
> 
> and indeed residue A279 has:
> 
> ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65   N
> 
> and
> ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20   N
> and the same for all the other atoms in the residues.
> 
> Searching the CCP4BB archives for "microheterogeneity" I see that this has
> been discussed before and apparently it should "just work" if there are alt
> atom indicators (check) and occupancies add up to <= 1 (check).  I must say I
> also was of the impression that it "just worked" so I'm a bit confused now
> why it doesn't.
> 
> Version info:
> DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
> ### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##
> 
> Is there some other hack I need to do to get it to work?
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
> 
> 
> 
> 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] Mean B factors and number of atoms (Refmac/baverage)

[Robbie Joosten]

Hi Julia,

For a table 1 you should make a sensible split of the atoms over which you 
calculate the mean. You might need to pool certain chains. There is not really 
convenient tool for that because the choice depends on the biology/biochemistry 
of your system. In practice, the easiest way is using the command line on just 
the ATOM/HETATM records (atom_site in mmCIF format) in which you are 
interested. Calculating the mean of a column of values is pretty 
straightforward in awk.
Example for all atoms in a PDB file:
grep ^[HA][TE][OT][MA] 100d_final.pdb  | cut -c 61-66 | awk '{sum = sum + $1} 
END {print sum/NR}'

Or mmCIF:
grep [HA][TE][OT][MA] /DATA/pdb_redo/00/100d/100d_final.cif |  awk '{sum = sum 
+ $16} END {print sum/NR}'

HTH,
Robbie

From: CCP4 bulletin board  On Behalf Of Julia Griese
Sent: Thursday, November 26, 2020 15:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage)

Hi all,

I’m writing a Table 1 and getting a bit confused when it comes to number of 
atoms and average B factors. Refmac has these in the table in the GUI, but the 
atom numbers in that table seem to include H, and I’m only interested in non-H 
atoms.
As an example, the PDB file says:

REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   ALL ATOMS: 8351

Which agrees with the total count minus TER cards, so that seems to be correct. 
However, the table in the GUI for this refinement run looks like this:

Chain mean B(No. atoms)
 AAA
41.4(   2193 )
BBB
57.7(   3499 )
CCC
57.7(   3499 )
DDD
41.7(   2212 )
EEE
60.3(923 )
FFF
60.6(920 )
aaa
55.4(   1323 )
ddd
56.0(   1346 )
GGG
34.3(  1 )
GaG
42.7(  1 )
GbG
34.3(  1 )
GcG
40.1(  1 )
GdG
40.6(  1 )
GeG
35.8(  1 )
GfG
34.2(  1 )
GgG
43.2(  1 )
HHH
40.6(136 )

You can easily see that this adds up to a lot more than 8351 atoms. The numbers 
for the G chain (metal ions) and the H chain (water) are correct, whereas the 
numbers for the macromolecule chains appear to include H. (If I run a 
refinement with H output to the final file, I get approximately the same number 
of atoms in total, though not quite.) But what I’m really interested in is of 
course the number of non-H atoms per chain. I don’t want to count all the atoms 
by hand…

I used to use baverage to calculate average B factors (and that would also give 
me the number of non-H atoms per chain), but can’t get that to work on the 
command line and can’t find it in the i2 GUI. I don’t have the old ccp4i 
anymore.

So if anyone could either tell me how to get baverage to work, or if there is 
another way to extract these numbers, I would much appreciate it!

Best,

Julia


--
Dr. Julia Griese
Assistant Professor
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4043
http://www.icm.uu.se/structural-biology/griese-lab/








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Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Robbie Joosten]

I’m with Dale on this, the scientifically prudent thing is to set the rules and 
then play by them. Not to change the rules as you go. Of course, in a teaching 
environment where you know the correct answer, it is good to be educational and 
learn how to dig a bit more.

However, in a scientific setting this digging is not to come to a strong 
conclusion, but only to see if you should pursue the project and do additional 
experiments (e.g. longer soaks or using a higher ligand concentration). In this 
case the topic starter has poor density and fitting the ligand and refining 
gives negative difference density. Surely that is not enough evidence to reject 
the null hypothesis “the ligand is not bound”. In other words, there is no 
strong evidence that the ligand is bound. Perhaps you can look at the occupancy 
, but that is probably as far as you should go. The polder map is useful to get 
rid of the effect of the solvent mask blurring actual ligand density. But after 
fitting the ligand you shouldn’t need the polder map. Blurring and sharpening 
is something to make sense of the density shape to better fit your ligand, not 
to conclude whether or not you ligand is there.

On a whole, for ligands we should try to stick to the so-called “bloody 
obvious” test: if the density is not bloody obvious, your ligand is not there. 
At least not all the time.

Cheers,
Robbie


From: CCP4 bulletin board  On Behalf Of Jon Cooper
Sent: Wednesday, November 25, 2020 05:20
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Hello Dale, the statistical rigour you describe is, of course, excellent, but 
in a learning environment, if someone gets a negative result, you have to go 
into overdrive to check that everything has been done correctly, since there is 
a fair chance that human error is the cause. It may be a terrible practice, but 
it would seem to be an important part of the process? Even as a relative 
newcomer to the field (well, since the mid-80's ;-) I have seen many people 
getting nothing in their initial difference maps, even if the ligand is there. 
Frequently it was just the contour level being too high and, depending on how 
far back you go, the solution varied from showing someone how to roll the mouse 
wheel in Coot to having the map recontoured at a computer centre 200 miles away 
and posted back on a magnetic tape, which took about 10 days - a timescale on 
which some people just gave up and did something else! I can't help thinking it 
would be a shame to robotically accept every negative result at face value, not 
least if you're doing something important like curing a pandemic. However, back 
to the original question which I think was whether polder map coefficients 
could be used as refinement targets and I think the answer to that one is 
probably 'no', at least in the X-ray field ;-)

Best wishes, Jon Cooper



 Original Message 
On 24 Nov 2020, 16:02, Dale Tronrud < 
de...@daletronrud.com> wrote:


Hi,

To me, this sounds like a very dangerous way to use this tool decide
if a ligand has bound. I would be very reluctant to modify my map with
a range of arbitrary parameters until it looked like what I wanted to
see. The sharpening and blurring of this tool is not guided or limited
by theory or data.

As you describe it, your choice of map is driven by its agreement
with your ligand, and the proper way to make this decision is the other
way around.

The original poster has the problem that their density does not have
the appearance they desire. They have chosen to run around trying to
find some way to modify the map to get a variant that does. This is a
terrible practice, since the final choice of map is being made in a
fashion that is dominated by bias.

I have no idea what sort of "structural characteristics" have
convinced this poster of the presence of their ligand despite the
absence of clear electron density. What other evidence does a
diffraction pattern give? The map is your best and only source of
information about your structure that you can get from the diffraction
pattern. (Mass spec and other experimental techniques could, of course,
be applied.)

I think we, as a community, could learn a few things from the
vaccine trial studies that are so much in the news now. In a modern
clinical trial, to avoid bias in the interpretation of the results, all
of the statistical procedures are decided upon BEFORE the study is even
began. This protocol is written down and peer reviewed at the start.
Then the study is performed and the protocol is followed exactly. If
the results don't pass the test, the treatment is not supported. There
is no hunting around, after the fact, for a "better" statistical measure
until one is found that "works".

This way of handling data analysis in clinical trials was adopted
after the hard lesson was learned that many trails could be reproduced,
their results were not.

Re: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

[Robbie Joosten]

Working on your bills with the entire bulletin board. Is that crowdsourcing or 
what? 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kevin
> Denkmann
> Sent: Tuesday, October 20, 2020 15:27
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf
> 'Rechnungen' ein.
> 
> 
> Kevin Denkmann shared a file with you
> 
> Here's the document that Kevin Denkmann shared with you.
> 
>  my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
>   Rechnungen
>   This link will work for anyone.
> Open  my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
> 
>   Privacy Statement  notifyp.svc.ms:443/api/v2/tracking/method/Click?mi=HgrSi7OfwUKiTn-
> 401hPpQ=PrivacyStatement=f97d4ae4336b3342c9a937ee3f36e84e
> u=https%3a%2f%2fprivacy.microsoft.com%2fprivacystatement%5c>
>   notifyp.svc.ms:443/api/v2/tracking/method/View?mi=HgrSi7OfwUKiTn-
> 401hPpQ>
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] over-fitting? over-refinement?

[Robbie Joosten]

A related way of looking at things is saying that you model is over-fitted when 
you increase your model's precision without (noticeably) gaining accuracy.

Ethan describes the cases in which you add a lot of parameters in you model. 
The test he describes in his paper works great, I use it all the time in 
pdb-redo. Pavel sent a lot of references to R-free which is used to test how 
predictive the model is. If R-free deviates too much from R, then apparently 
your model is not predictive enough for additional data (so it's too precise or 
not accurate enough). If we relate accuracy to R-free and the predictiveness of 
the model, then where does the precision com from if you do not change the 
number of model parameters? We always give coordinates and B-factors with the 
same precision in our models, don't we? Well yes, but we change other aspects 
of the model's precision by adding restraints (effectively improving the 
degrees of freedom of the model: Occam's Razor). For instance we have 
restraints to reduce the range that bond lengths can have in our model with 
respect to their "known" standard deviation. Or we reduce the differences 
between things we expect to be very similar with NCS restraints. That is why we 
validate models by looking at scores like the bond length rmsZ: we check 
whether the model is not too precise overall. If one bond is much longer or 
shorter than expected, this can still be right. If most of them are, then 
something is going on and your model may be too precise. Same goes for your 
Ramachandran plot, a single outlier may not be a problem, but if all residues 
are off a lot you should worry. That is why we have been advocating the 
Ramachandran Z-score (also see the recent paper by the Phenix and PDB-REDO 
teams).

All of the things are related to the degrees of freedom of your system 
(obeservations - parameter + some_weight*restraints). Make sure you do not have 
too many parameters overall, improve the degrees of freedom by adding 
restraints. You can balance precision and accuracy by changing the weights on 
the restraints. And you check the accuracy by looking at the deviation of R and 
R-free.

HTH,
Robbie 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ethan A
> Merritt
> Sent: Tuesday, October 20, 2020 06:04
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] over-fitting? over-refinement?
> 
> On Monday, 19 October 2020 20:27:04 PDT Sam Tang wrote:
> > Hi, the question may be a bit weird, but how do you define 'over-fitting'
> > in the context of structure refinement? From users' perspective the
> > practical aspect is to 'fit' the model into the density. So there
> > comes this question from our juniors: fit is fit, how is a model over-fit?
> 
> That is a good question, not asked as many times as it should be.
> There are several validation techniques, tools, and indicators.
> You are probably at least familiar with Rfree as an indicator.
> But you are asking the deeper question "what is it that makes it over-fit".
> 
> I suggest that the best starting point for thinking about it is Occam's Razor,
> specifically the rephrasing by Albert Einstein:
>"Everything should be made as simple as possible,
> but no simpler."
> 
> In applying this to considering a crystallographic model, that can be
> translated as "the number of parameters used in the model should be as
> small as possible, but no smaller".
> 
> For example, if your structure is a homo-dimer you have a choice of
> modelling each monomer separately or modelling only one monomer and
> then describing how to generate the second by some symmetry operation.
> Modeling each monomer independently will obviously require twice as many
> parameters as modelling only one.
> The guidance from Occam + Einstein is that the simpler (== smaller) model is
> better, but only if it in fact adequately explains your observations.
> 
> Ah, but how do you know if the simpler description is "adequate"?
> That's where specific statistical tests and quality measures come in.
> From hundreds of thousands of previous crystal structures we have a good
> idea of what the R-factor for a good model is expected to be.
> Does your simple model have a good R-factor?   Good enough?
> If you refine the more complicated (twice as big) model does it have a better
> R-factor?  If not then clearly all those extra parameters are useless and the
> model is over-fit.
> More typically the R-factor for the more complicated model will be a little 
> bit
> better.  But "a little bit" is not very convincing.
> So we need some statistical test to ask if the model is
> _significantly_ better.   I won't delve into statistics here,
> but that's the philosophical approach.
> 
> I wrote a paper some years ago trying to lay this out as clearly as I could
> while focusing on a common choice made by crystallographers as to how to
> choose or refine B factors.  The logic and statistical approach is valid for
> many other choices 

[ccp4bb] PDB-REDO downtime on October 17th

[Robbie Joosten]

Dear BB'ers,

Due to electrical maintenance and testing at the Netherlands Cancer Institute, 
the PDB-REDO server and databank will be unavailable on Saturday October 17th 
from approximately 6:00h to 16:00h CEST (Amsterdam local time). 

Sorry for the inconvenience,
Robbie



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Robbie Joosten]

Indeed, and that is why testing new developments in courses is so important 
because there you get naïve users. Obviously, this has been very difficult this 
year. It is also exactly the reason why you do need to have developers at 
courses, not just power users. 

For those struggling to get used to Coot 0.9 there are few tips:
1) Drag atoms where you want them to go, not beyond where you want them. I.e. 
don't "overdrag" like you used to do in Coot.
2) Try to get close to the right answer first by rigid body movement. This is 
particularly useful for ligands.
3) Practice*. The C-termini in PDB entry 1ggx are nice to practice resisting to 
overdrag.

Cheers,
Robbie

* Ling Ling practices 40 hours a day!

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Tim
> Gruene
> Sent: Wednesday, September 9, 2020 23:01
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8
> 
> Hi Eike,
> 
> one of the points is that, only because you got used to a certain operation
> (over many years after someone showed it to you), does not mean it is
> intuitive. This could be judged by e.g. showing an ignorant user both
> methods and let the person judge which one is easier to use...
> 
> Cheers,
> Tim
> 
> On Wed, 9 Sep 2020 20:27:55
> + "Schulz, Eike-Christian"  wrote:
> 
> > Hi Tim,
> >
> > I don't think that metaphor is quite correct. To me it seems that no
> > matter what button you pushed you got coffee. In my opinion intuitive
> > software is a blessing and should not easily be disregarded.
> >
> > But as I said before, I am happy to read into new stuff.
> >
> > Also there seem to be mixed experiences here. Might this be
> > map-resolution related ?
> >
> > Best,
> >
> > Eike
> >
> >
> >
> > -Original Message-
> > From: CCP4 bulletin board  on behalf of Georg
> > Zocher  Reply to: Georg Zocher 
> > Date: Wednesday, 9. September 2020 at 22:17
> > To: "CCP4BB@JISCMAIL.AC.UK" 
> > Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot
> > 0.8
> >
> > Dear Herman,
> >
> > Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:
> > > The old real-space refinement was intuitive and easy to use and
> > > did exactly what the user expected, without having to consult
> > > the manual! The result might not have been perfect, but was
> > > good enough for subsequent Refmac, Buster, Phenix refinement.
> >
> > That fits perfectly to my user experience with RSR in coot 0.8.x.
> > and also explains why at least a number of people having some issues
> > with the new RSR.
> >
> > All the best,
> >
> > Georg
> >
> >
> >
> ###
> ###
> > ##
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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> >
> >
> ###
> ###
> > ##
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> 
> 
> 
> --
> --
> 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] taking information from a deposited structure

[Robbie Joosten]

Dear Kahkashan,That is totally fine as long as you make it clear that you used this PDB entry. That's what the PDB is for.Just make sure you check the model with the electron density from EDS or pdb-redo. Cheers,RobbieOn 9 Sep 2020 07:41, Firdous Tarique  wrote:Dear CCP4 community members.I have solved  a crystal structure of a protein and am now trying to get a structure with a ligand bound to it, but so far unsuccessful. A homologous structure with the same ligand is present in the RCSB PDB (un published). Is it permissible to fetch structural information from that unpublished data and use it for docking and simulation studies with my protein? Will it be copyright infringement or it is just a normal thing.  I will be mentioning in my manuscript that I have used this unpublished structure (deposited by this author) for these studies. BestKahkashan


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Re: [ccp4bb] metal coordination at low resolution - restraints

[Robbie Joosten]

Yes, and the Zn is tetrahedral with a vacancy which makes then angles a bit 
more open. It's a good thing insulin makes nice crystals 

Cheers,
Robbie

> -Original Message-
> From: Eleanor Dodson 
> Sent: Tuesday, September 8, 2020 12:59
> To: Robbie Joosten 
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
> 
> I guess I have lived with Zn since I first learnt what a crystal was - ZN is 
> part
> of insulin secretion and whether it is or is not present is fundamental to the
> biochemistry..
> 
> I agree things have to be handled case by case - For insulin the three HIS are
> generated by symmetry and that causes horrible headaches for any restraint
> dictionary..
> And for Jan's case the resolution is excellent and the main links very clear. 
> (In
> fact they were not restrained but all distances finish up near to 2A as
> expected.) However maybe something can be learnt from this structure
> which would help the query which started us off!
> Eleanor
> 
> On Tue, 8 Sep 2020 at 11:49, Robbie Joosten  <mailto:robbie_joos...@hotmail.com> > wrote:
> 
> 
>   Hi Jan,
> 
>   If you want targets for your metal site you could have a look at
> MetalPDB (http://metalweb.cerm.unifi.it/). That has good tools to find
> similar sites and get some statistics you can use to generate case-specific
> restraints.
> 
>   Cheers,
>   Robbie
> 
>   > -Original Message-
>   > From: CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Garib
>   > Murshudov
>   > Sent: Tuesday, September 8, 2020 12:44
>   > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>   > Subject: Re: [ccp4bb] metal coordination at low resolution -
> restraints
>   >
>   > Hi Jan,
>   >
>   >
>   >
>   >
>   >   On 8 Sep 2020, at 11:39, Jan Dohnalek
> mailto:dohnalek...@gmail.com>
>   > <mailto:dohnalek...@gmail.com
> <mailto:dohnalek...@gmail.com> > > wrote:
>   >
>   >   These are structural.
>   >
>   >
>   > Are they tetrahedral or octahedral? From the list of neighbours
> they do not
>   > look like tetrahedral. Some of them do look like octahedral.
>   >
>   >
>   >   They form the active site of our enzyme.
>   >
>   >
>   > So,are they  involved in reaction?
>   >
>   >
>   >   Normally there is no need to restrain these, they "behave".
>   >
>   >   But in general having such standard "restraint angles" available
>   > would be of use, I agree.
>   >
>   >
>   >
>   > For tetrahedral Zn we do have “bonds” and “angles” between Zn
> and
>   > coordinating residues. For general solution we need a bit different
> approach
>   > (e.g. coordination analysis).
>   >
>   >
>   >
>   > Regards
>   > Garib
>   >
>   >
>   >
>   >
>   >   Jan
>   >
>   >
>   >   On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov> lmb.cam.ac.uk <http://lmb.cam.ac.uk>  <mailto:garib@mrc-
> lmb.cam.ac.uk <mailto:ga...@mrc-lmb.cam.ac.uk> > > wrote:
>   >
>   >
>   >   What are these numbers?
>   >
>   >   If I understand these numbers correctly: none of your Zn
>   > atoms is structural (4 coordinated tetrahedral). If that is the case
> then you
>   > need specific links or restraints. If my reading of your numbers is
> correct
>   > then there could be some chemistry change of the surrounding
> residues.
>   >
>   >   If it is not structural Zn then it is likely that 
> coordination is
> 6.
>   > But without seeing coordinates and maps it is difficult to say what
> is there.
>   >
>   >   Regards
>   >   Garib
>   >
>   >
>   >
>   >   On 8 Sep 2020, at 11:11, Eleanor Dodson
>   >  <mailto:eleanor.dod...@york.ac.uk>  <mailto:eleanor.dod...@york.ac.uk
> <mailto:eleanor.dod...@york.ac.uk> > > wrote:
>   >
>   >   Hmm - here is my problem - a list of ZN 
> contacts for
>   > the two molecules..
>   >   residue 602 is a phosp

Re: [ccp4bb] metal coordination at low resolution - restraints

[Robbie Joosten]

  Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z
> 1.009.22
>Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z
> 1.009.70
>Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z
> 0.709.58
> 
> 
>Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z
> 1.00   10.80
>Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z
> 1.00   10.65
>Z  403 ZN   B   D  172 OD2  B  2.089 X,Y,Z
> 1.00   13.12
>Z  403 ZN   B   Z  601 O4   B  1.938 X,Y,Z
> 0.70   14.10
>Z  403 ZN   B   O  825 OC  2.322 X,Y,Z
> 0.20   10.61
>   ~
> 
>   On Tue, 8 Sep 2020 at 10:47, Garib Murshudov
> mailto:ga...@mrc-lmb.cam.ac.uk> > wrote:
> 
> 
>   Hi Robbie and Eleanor
> 
>   There are links for Zn-His and Zn-Cys. They
> meant to be used automatically, obviously something is not entirely right.
> 
>   Link names are:
>   ZN-CYS
> 
> 
>   It has a bond between Zn and S as well as an
> angle:
>   ZN-CYS   1 ZN  2 SG  2 CB  109.000
> 3.000
> 
>   This also removes H of Cys to make covalent
> bond between Zn and Cys.
> 
>   Similar links are available for Zn and His ND1
> and Zn - HIS NE2
>   Link names are:
> 
>   ZN-HISND
>   ZN-HISNE
> 
> 
>   Again these links have angles between Zn and
> atoms of His.
> 
> 
>   Angle centred at Zn is missing. But these
> distances and angles defined in the link it should work fine.
> 
> 
>   Regards
>   Garib
> 
> 
> 
> 
>   On 8 Sep 2020, at 10:40, Robbie
> Joosten  <mailto:robbie_joos...@hotmail.com> > wrote:
> 
>       Hi Elanor,
> 
>   The distances are in the dictionaries
> but the angles involve three different residues so these cannot be in the
> current dictionary. We could add the program that generates these
> restraints to CCP4 though.
> 
>   Cheers,
>   Robbie
> 
> 
> 
>   -Original Message-
>   From: Eleanor Dodson
> mailto:eleanor.dod...@york.ac.uk> >
>   Sent: Tuesday, September 8, 2020
> 11:38
>   To: Robbie Joosten
> mailto:robbie_joos...@hotmail.com> >;
> Garib N Murshudov
>    <mailto:ga...@mrc-lmb.cam.ac.uk> >
>   Cc: CCP4BB@JISCMAIL.AC.UK
> <mailto:CCP4BB@JISCMAIL.AC.UK> ; Robert Nichollslmb.cam.ac.uk
> <http://lmb.cam.ac.uk/> >
>   Subject: Re: [ccp4bb] metal
> coordination at low resolution - restraints
> 
>   Robbie - could that be added to the
> distributed dictionaries? Zn binding is
>   common and at low resolution
> distance restraints are not enough..
>   Eleanor
> 
>   On Tue, 8 Sep 2020 at 10:33, Robbie
> Joosten  <mailto:robbie_joos...@hotmail.com>
> 
>   <mailto:robbie_joos...@hotmail.com> > wrote:
> 
> 
>   Hi Anna,
> 
>   Yes you can do this in Refmac by
> adding external restraints. If you
>   have structural Zinc sites (Zn
> coordinated by 4 histidines or cysteines)  you
>   can also use PDB-REDO to generate
> the restraints automatically. The
>   restraints are written to the output
> so you can continue using them in
>   Refmac.
> 
>   HTH,
>   Robbie
> 
>   > -Original Message-
>

Re: [ccp4bb] metal coordination at low resolution - restraints

[Robbie Joosten]

Hi Elanor,

The distances are in the dictionaries but the angles involve three different 
residues so these cannot be in the current dictionary. We could add the program 
that generates these restraints to CCP4 though.

Cheers,
Robbie

> -Original Message-
> From: Eleanor Dodson 
> Sent: Tuesday, September 8, 2020 11:38
> To: Robbie Joosten ; Garib N Murshudov
> 
> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls  lmb.cam.ac.uk>
> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
> 
> Robbie - could that be added to the distributed dictionaries? Zn binding is
> common and at low resolution distance restraints are not enough..
> Eleanor
> 
> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten  <mailto:robbie_joos...@hotmail.com> > wrote:
> 
> 
>   Hi Anna,
> 
>   Yes you can do this in Refmac by adding external restraints. If you
> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines)  you
> can also use PDB-REDO to generate the restraints automatically. The
> restraints are written to the output so you can continue using them in
> Refmac.
> 
>   HTH,
>   Robbie
> 
>   > -Original Message-
>   > From: CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of anna
>   > anna
>   > Sent: Tuesday, September 8, 2020 11:28
>   > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>   > Subject: [ccp4bb] metal coordination at low resolution - restraints
>   >
>   > Dear all,
>   >
>   > quickly: is there a way to restrain metal coordination geometry
> (even angles)
>   > in refmac?
>   >
>   > I am refining a low resolution structure (3.3A) with 2 zinc binding
> sites.
>   > I am pretty sure about metal position (strong anomalous signal)
> and what
>   > are the residues involved in coordination since I solved the apo-
> structure at
>   > good resolution and Zn-binding does not induce huge structural
> variations.
>   > However, as you can imagine, electron density is poorly defined
> and Refmac
>   > gives a very distorted coordination geometry.
>   > I noticed that in phenix it is possible to generate restraints with
> readyset but
>   > I'd like to work with refmac.
>   >
>   > Many thanks for your suggestions.
>   >
>   > Cheers,
>   > Anna
>   >
>   > 
>   >
>   >
>   > 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:
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Re: [ccp4bb] metal coordination at low resolution - restraints

[Robbie Joosten]

Hi Anna,

Yes you can do this in Refmac by adding external restraints. If you have 
structural Zinc sites (Zn coordinated by 4 histidines or cysteines)  you can 
also use PDB-REDO to generate the restraints automatically. The restraints are 
written to the output so you can continue using them in Refmac.

HTH,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of anna
> anna
> Sent: Tuesday, September 8, 2020 11:28
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] metal coordination at low resolution - restraints
> 
> Dear all,
> 
> quickly: is there a way to restrain metal coordination geometry (even angles)
> in refmac?
> 
> I am refining a low resolution structure (3.3A) with 2 zinc binding sites.
> I am pretty sure about metal position (strong anomalous signal) and what
> are the residues involved in coordination since I solved the apo-structure at
> good resolution and Zn-binding does not induce huge structural variations.
> However, as you can imagine, electron density is poorly defined and Refmac
> gives a very distorted coordination geometry.
> I noticed that in phenix it is possible to generate restraints with readyset 
> but
> I'd like to work with refmac.
> 
> Many thanks for your suggestions.
> 
> Cheers,
> Anna
> 
> 
> 
> 
> 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] Omega angles with molprobity

[Robbie Joosten]

Hi Joana,

By default it only lists non-trans peptides. Theis command worked for me:
molprobity.omegalyze tempdir/3bwh/pdb3bwh.pdb nontrans_only=False

Cheers,
Robbie

> -Original Message-
> From: Joana Pereira 
> Sent: Friday, September 4, 2020 12:04
> To: Robbie Joosten ;
> CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Omega angles with molprobity
> 
> Hi Robbie,
> 
> Thanks for the quick response :) That was my first try but it does not list me
> the angles.. see the output below:
> 
> Starting molprobity.omegalyze
> on Fri Sep  4 12:00:35 2020 by jpereira
> ===
> 
> 
> Processing files:
> ---
> 
>   Found model, .pdb
> 
> Processing PHIL parameters:
> ---
> 
>   No PHIL parameters found
> 
> Final processed PHIL parameters:
> ---
>   data_manager {
> model {
>   file = ".pdb"
> }
> default_model = ".pdb"
>   }
> 
> 
> Starting job
> ===
> 
> residues:type:omega:conformation:mc_bmax
> SUMMARY: 0 cis prolines out of 5 PRO
> SUMMARY: 0 twisted prolines out of 5 PRO
> SUMMARY: 0 other cis residues out of 140 nonPRO
> SUMMARY: 0 other twisted residues out of 140 nonPRO
> 
> ===
> 
> 
> 
> What I would like to have is a per residue assignment of omega angles, as
> molprobity.ramanalyse does. Of course i could code it, but I was trying to
> avoid that ;)
> 
> 
> Cheers,
> 
> Joana
> 
> 
> 
> 
> On 04.09.20 11:45, Robbie Joosten wrote:
> 
> 
>   Hi Joana,
> 
>   molprobity.omegalyze seems to do what you want. Just run it on the
> command prompt.
> 
>   Cheers,
>   Robbie
> 
> 
>   -Original Message-
>   From: CCP4 bulletin board 
> <mailto:CCP4BB@JISCMAIL.AC.UK>  On Behalf Of Joana
>   Pereira
>   Sent: Friday, September 4, 2020 11:29
>   To: CCP4BB@JISCMAIL.AC.UK
> <mailto:CCP4BB@JISCMAIL.AC.UK>
>   Subject: [ccp4bb] Omega angles with molprobity
> 
>   Dear all,
> 
>   Does anyone know which molprobity tool in ccp4/bin lists
> the omega angles
>   for each residue? I see Phenix provides a comprehensive
> validation based on
>   Molprobity and, from what I understand, lists the omega
> angles for each
>   residue. However, I am having troubles to find which
> molprobity tool
>   provides that info. Any idea?
> 
>   Many thanks!
> 
>   Best wishes
> 
>   Joana Pereira
> 
>   --
>   Postdoctoral Researcher
>   Department of Protein Evolution
> 
>   Max Planck Institute for Developmental Biology Max-Planck-
> Ring 5
>   72076 Tübingen
>   GERMANY
> 
> 
>   
> ###
>   #
> 
>   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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> 
>   
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
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> --
> Postdoctoral Researcher
> Department of Protein Evolution
> 
> Max Planck Institute for Developmental Biology Max-Planck-Ring 5
> 72076 Tübingen
> GERMANY



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Re: [ccp4bb] Omega angles with molprobity

[Robbie Joosten]

Hi Joana,

molprobity.omegalyze seems to do what you want. Just run it on the command 
prompt.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Joana
> Pereira
> Sent: Friday, September 4, 2020 11:29
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Omega angles with molprobity
> 
> Dear all,
> 
> Does anyone know which molprobity tool in ccp4/bin lists the omega angles
> for each residue? I see Phenix provides a comprehensive validation based on
> Molprobity and, from what I understand, lists the omega angles for each
> residue. However, I am having troubles to find which molprobity tool
> provides that info. Any idea?
> 
> Many thanks!
> 
> Best wishes
> 
> Joana Pereira
> 
> --
> Postdoctoral Researcher
> Department of Protein Evolution
> 
> Max Planck Institute for Developmental Biology Max-Planck-Ring 5
> 72076 Tübingen
> GERMANY
> 
> ###
> #
> 
> 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] PDB-REDO downtime

[Robbie Joosten]

Hi everyone,Due to major electrical work at our institute, PDB-REDO will be down from Sunday August 16th 20:00h CET to Tuesday August 18th 11:00h CET.Any calculations still running at the start of the downtime will be restarted once we are back online, but feel free to email me to remind me on Tuesday. On behalf of the PDB-REDO team, sorry for the inconvenience,Robbie


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Re: [ccp4bb] Quote source inquiry

[Robbie Joosten]

I suppose that this is where the phrase "Mind your own beeswax" comes from 
 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Edward
> Snell
> Sent: Thursday, July 16, 2020 16:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Quote source inquiry
> 
> Not completely related to the question but at one particular European
> synchrotron there were a group of beamline scientists that also kept honey
> bees. The wax from each hive gave very beautiful powder diffraction
> patterns with the scattering being similar but distinctive to each hive. I was
> fortunate to observe this before my data collection - this was their
> calibration of the beam center.
> 
> In the US, many years before BluIce there was a 'jiffy' software routine that
> would take a powder pattern and accurately calculate the beam center. This
> saved one of our structures. Wax, silicon powder, and other test samples
> were used. If I remember correctly cryo-vials had a powder signature and a
> magnet with part of a vial glued to it became part of the tool kit when one
> would still routinely travel to the beamline.
> 
> I've been saved once with the powdered silicon. We had a hutch that was
> completely empty when we arrived due to an unanticipated emergency. A
> week of beamtime turned into an amazing educational opportunity to install
> and align the diffractometer. The powder data proved very useful in the
> energy calibration. After installation and alignment, unbelievably we were
> able to collect our data and get a publication from it.
> 
> Best,
> 
> Eddie
> 
> Edward Snell Ph.D.
> 
> Director of the NSF BioXFEL Science and Technology Center President and
> CEO Hauptman-Woodward Medical Research Institute BioInnovations
> Chaired Professorship, University at Buffalo, SUNY
> 700 Ellicott Street, Buffalo, NY 14203-1102 hwi.buffalo.edu
> Phone:   (716) 898 8631 Fax: (716) 898 8660
> Skype:eddie.snell Email: esn...@hwi.buffalo.edu
> Webpage: https://hwi.buffalo.edu/scientist-directory/snell/
> 
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Harry Powell - CCP4BB
> Sent: Thursday, July 16, 2020 7:26 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Quote source inquiry
> 
> Hi
> 
> Does anyone bother collecting a powder image (e.g. Si powder) these days
> so they actually have a reference that can be used to check both the
> wavelength and the beam centre? Or is this considered just something that
> old folk do?
> 
> Harry
> 
> > On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt
>  wrote:
> >
> > There was a case a few years ago (not too many though) where a 1.6 Å
> structure had been solved using an incorrect value for the wavelength (~5%
> too low, leading to a cell that was slightly too small for its contents to be
> comfortable). It was later corrected so we could compare their validation
> statistics. Some interesting observations:
> >
> > - the geometry had been very tightly restrained so that didn't give a
> > clue  about the cell error (WhatCheck only suggested a very small
> > change)
> >
> > - somewhat surprisingly (I thought) the Ramachandran plot did not
> > improve in  the correct model (0.3% outliers in the wwPDB validation
> > report), and the  sidechain rotamer outliers even got worse (from 1.5
> > to 2.5 %)
> >
> > - the map looked surprisingly good for the incorrect cell
> >
> > - however, RSR-Z told clearly that the map was not good enough for the
> > claimed  resolution - the model had 24% outliers! (3% in the corrected
> > model which  still only put it at the ~50th percentile)
> >
> > - another good indicator was the clashscore (went from 44 to 7)
> >
> > - the original model did not include an Rfree, but the R-value (>0.3
> > at 1.6Å
> >  resolution) ought to have provided a clue to the crystallographers
> > and  reviewers one would think
> >
> > It would be interesting to see what would happen if the wavelength would
> be set 5% too high.
> >
> > --Gerard
> >
> >
> >
> > On Thu, 16 Jul 2020, Clemens Vonrhein wrote:
> >
> >> Hi Robbie,
> >>
> >> On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:
> >>> At the same time if you have a a more relaxed approach to restraints
> >>> than you might find systematic deviations in bond lengths. A test
> >>> for that has been in WHAT_CHECK for decades and it actually works
> >>> surprisingly well to detect cell dimension problems.
> >>
> >> In

Re: [ccp4bb] Quote source inquiry

[Robbie Joosten]

I don't know what the return on investment would be, but after establishing 
that there are cell dimension deviations one should actually try to find the 
source of the problem. If it is the reported geometry of the experiment than it 
is just a matter of changing the cell dimension, but if the wavelength come 
into play as Clemens pointed out (hooray for home sources) one should also 
correct the wavelength in order to get better scattering factors. If you don't 
have ice rings as a reference can you still do that? Perhaps refine f' and f''. 
Has anyone does that in a systematic way?

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Eleanor
> Dodson
> Sent: Thursday, July 16, 2020 12:57
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Quote source inquiry
> 
> Hmm - remember Gerard, the EU Validation initiative in the 1990s? We
> analysed these effects, or at least Victor Lamsin did, and we applauded him.
> Cheers Eleanor
> 
> On Thu, 16 Jul 2020 at 11:52, Clemens Vonrhein
> mailto:vonrh...@globalphasing.com> >
> wrote:
> 
> 
>   Hi Robbie,
> 
>   On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:
>   > At the same time if you have a a more relaxed approach to
> restraints
>   > than you might find systematic deviations in bond lengths. A test
>   > for that has been in WHAT_CHECK for decades and it actually
> works
>   > surprisingly well to detect cell dimension problems.
> 
>   Indeed.
> 
>   > That said, the problem is uncommon now.
> 
>   Not so sure about that: we all rely on an accurate value of the
>   energy/wavelength from the instrument/beamline - and if that is off
>   (for whatever reasons) it will result in incorrect cell dimensions and
>   a systematic deviation from the various restraints.
> 
>   This would even affect the best experiment done on the best crystal
>   ... so fairly easy to spot at the refinement stage, especially if such
>   an energy/wavelength offset is constant over a long period of time
> on
>   a given instrument. To spot this at the data collection stage one
>   would hope that at some point a crystal with very pronounced ice-
> rings
>   will be looked at properly (and the fact these are not where we
> expect
>   them to should cause some head-scratching).
> 
>   Cheers
> 
>   Clemens
> 
>   
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
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> 
> 
> 
> 
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Re: [ccp4bb] Quote source inquiry

[Robbie Joosten]

Hi Ian,

Errors in cell dimensions can have a large effect in MX with certain refinement 
doctrines. The school of "bond length rmsd must be $NUMBER" (which is still 
going strong unfortunately) will suffer from poor R-factors because the target 
cannot be satisfied without harming the fit to the data. At the same time if 
you have a a more relaxed approach to restraints than you might find systematic 
deviations in bond lengths. A test for that has been in WHAT_CHECK for decades 
and it actually works surprisingly well to detect cell dimension problems. That 
said, the problem is uncommon now.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ian
> Tickle
> Sent: Wednesday, July 15, 2020 20:25
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Quote source inquiry
> 
> 
> Hi,
> 
> There's one big difference between macromolecular and small molecule
> refinement: except at ultra-high resolution the bond lengths in the former
> are almost always strongly restrained, whereas those in the latter are almost
> without exception completely unrestrained (except possibly bond lengths to
> H atoms in XRD).  In other words, MX accurately determines the orthogonal
> atomic co-ordinates, whereas XRD accurately determines their fractional co-
> ordinates (it's no accident that the different programs output co-ordinates in
> those formats).
> 
> This means that since the cell dimensions are then used to convert fractional
> to orthogonal in XRD, the final bond lengths will be much more sensitive to
> errors in the cell dimensions, so having accurate cell dimensions is more
> critical if you want accurate bond lengths (e.g. for use as restraints in 
> MX!).
> Obviously there's also a limit to the errors in the cell dimensions that can 
> be
> tolerated in MX: large errors will lead to errors in calculated d* values and
> hence the scattering factors, which is likely to have a significant effect, 
> and
> there may be issues with VdW repulsions if the cell is too small (though it's
> relatively easy for the structure to accommodate that).
> 
> As Philip pointed out, the bond lengths will be totally insensitive to errors 
> in
> the uncertainties of the cell dimensions, whether artificially introduced or
> poorly estimated from the data.  I don't know of any MX refinement
> program (other than Shel-X) that takes the uncertainties in the cell
> dimensions into account, even assuming that you have accurate values for
> them.
> 
> Also you should be careful not to confuse uncertainty (imprecision) with
> error (inaccuracy).  The 'standard uncertainty' (s.u.) is the experimental
> estimate of the 'standard deviation' (in the error)
> (https://physics.nist.gov/cgi-bin/cuu/Info/Constants/definitions.html), and
> the old term 'estimated standard deviation' (e.s.d.) was deprecated in 1993
> (http://scripts.iucr.org/cgi-bin/paper?S0108767395002340).  You can have
> an error in an uncertainty (which is what you were introducing in your test),
> but you can't have an uncertainty in an error, since errors are by their 
> nature
> unknown anyway!
> 
> It goes without saying that it's not a good idea to use bond lengths from a
> restrained refinement as restraints in other refinements!
> 
> Cheers
> 
> -- Ian
> 
> 
> On Wed, 15 Jul 2020 at 17:56, Jeffrey B Bonanno
>   > wrote:
> 
> 
>   Hi Phil,
> 
> 
> 
>   Being young and impressionable, I only changed ZERR, and you are
> quiet right the result is the rigorous and expected error propagation of
> shelxl. Of course the more fun experiment would be in systematically
> changing various values in UNIT to watch the molecule distort.
> 
> 
> 
>   Hope all is well,
> 
>   jbb
> 
> 
> 
>   Jeffrey B. Bonanno, Ph.D.
> 
>   Department of Biochemistry
> 
>   Albert Einstein College of Medicine
> 
>   1300 Morris Park Avenue
> 
>   Bronx, NY 10461
> 
>   off. 718-430-2452 fax. 718-430-8565
> 
>   email jeffrey.bona...@einsteinmed.org
> 
> 
> 
> 
>   From: Jeffrey, Philip D. 
>   Sent: Wednesday, July 15, 2020 12:47 PM
>   To: CCP4BB@JISCMAIL.AC.UK  ;
> Jeffrey B Bonanno   >
>   Subject: Re: [ccp4bb] Quote source inquiry
> 
> 
> 
> CAUTION: This email comes from an external source; the attachments and/or
> links may compromise our secure environment. Do not open or click on
> suspicious emails. Please click on the “Phish Alert” button on the top right 
> of
> the Outlook dashboard to report any suspicious emails.
> 
>   :: took a working dataset and increased (only) the error on unit cell
> dimensions in the instruction file for the final round of full matrix :: least
> squares refinement in shelxl. Sure enough, the errors on the bonds and
> angles shot up. I was more careful
> 
> 
> 
>   Question: did you change the unit cell dimensions (UNIT) 

[ccp4bb] B-factor distributions

[Robbie Joosten]

Posted on behalf of Gert Vriend:

This article didn't make it to Nature Methods (...), but might be of interest 
to theoreticians interested in B-factor distributions:
 https://journals.calstate.edu/pump/article/view/2409/2168 

Gert Vriend



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Re: [ccp4bb] Completeness question

[Robbie Joosten]

Hi Clemens,

Thanks for pointing out the table in the PDBpeep log file. It has the data I 
need and since the issue only applies to deposited PDB entries it does the 
trick quite nicely.

Cheers,
Robbie

> -Original Message-
> From: Clemens Vonrhein 
> Sent: Wednesday, June 3, 2020 14:18
> To: Robbie Joosten 
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Completeness question
> 
> Dear Robbie,
> 
> On Sat, May 30, 2020 at 08:36:06AM +, Robbie Joosten wrote:
> > I've been looking at some recent PDB entries that have much lower
> > spherical) completeness than reported in the coordinate file. One
> > reason for this is that the data were anisotropicly truncated, another
> > reason is some mess-up with the deposition of the reflection data.
> > There is a lot of discussion about the former practice and I don't
> > want to go in to that, but the second one is obviously an error. Now
> > how do I distinguish these cases?
> >
> > Sometimes, you can look at the reported number of reflections and
> > compare that to the deposited reflection file and you will find that
> > something has clearly gone wrong. However, the reported number of
> > reflections is not entirely reliable because of other issues so I'd
> > rather not use it. If you use PDBpeep (e.g. for 6rjy) you can see
> > something is wrong, but that is completely visual. Is there a tool in
> > CCP4 that reports both spherical and ellipsoidal completeness (on
> > merged reflection data)? That would make it easy to distinguish such
> > cases.
> 
> One needs a description of the anisotropy in a form that allows for a simple
> computation ("Is a reflection above a significance limit or
> not?") to relate this to the completeness of reflections above such a
> significance level. That model could e.g. be the ellipsoid fitted to the
> significance (local ) cutoff surface as done by STARANISO [1]. You can
> see that information e.g. at the PDBpeep server [2]:
> 
>   http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6rjy
> 
> as
> 
>   Diffraction limits & principal axes of ellipsoid fitted to diffraction 
> cut-off
> surface:
> 
>   1.747 1.   0.   0.   a*
>   1.777 0.   1.   0.   b*
>   1.465 0.   0.   1.   c*
> 
> Of course, if this information is already present in deposited PDB entries of
> interest, no additional computation is required. We are currently working
> with our colleagues from the PDBx/mmCIF working group on definitions and
> items that would extend the current PDBx/mmCIF dictionary so that the
> above information could be deposited to and retrieved from the PDB
> database.
> 
> In any case, this information is then used for computation of the spherical
> and ellipsoidal completness e.g. within STARANISO - see link to the
> "complete log file" at the bottom of the page:
> http://staraniso.globalphasing.org/PDB/6rjy.log. It contains a table
> ("Statistics for isotropic, anisotropic & ellipsoidal diffraction
> cut-offs") where Cmeas_sph and Cmeas_ell should give the above
> information (showing clearly that for 6rjy something else went wrong during
> deposition).
> 
> If there is unmerged data deposited, one could give that ellipsoid description
> e.g. to MRFANA [3] via
> 
>   mrfana -ell 1.747 1.0 0.0 0.0 1.777 0.0 1.0 0.0 1.465 0.0 0.0 1.0
> unmerged.mtz
> 
> to get the same information (but maybe use different binning, limit
> resolution ranges etc).
> 
> Cheers
> 
> Clemens, Claus, Ian & Gerard
> 
> [1] http://staraniso.globalphasing.org/
> [2] http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi
> [3] https://github.com/githubgphl/MRFANA, a result of the Data Quality
> Metrics Workshop organised by Global Phasing at the ESRF in April
> 2019



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Re: [ccp4bb] Completeness question

[Robbie Joosten]

I fully agree. Unfortunately, not everyone does that so cases like I described will keep appearing. Cheers,RobbieOn 30 May 2020 16:40, Eleanor Dodson  wrote:My pennysworth. If you find your maps look better after the anisotroy correction use it, but it may be helpful to those wo want to mine your data if you deposit the whole sphere..eleanorOn Sat, 30 May 2020 at 09:36, Robbie Joosten <robbie_joos...@hotmail.com> wrote:Hi Everyone,

I've been looking at some recent PDB entries that have much lower spherical) completeness than reported in the coordinate file. One reason for this is that the data were anisotropicly truncated, another reason is some mess-up with the deposition of the reflection data. There is a lot of discussion about the former practice and I don't want to go in to that, but the second one is obviously an error. Now how do I distinguish these cases?

Sometimes, you can look at the reported number of reflections and compare that to the deposited reflection file and you will find that something has clearly gone wrong. However, the reported number of reflections is not entirely reliable because of other issues so I'd rather not use it. If you use PDBpeep (e.g. for 6rjy) you can see something is wrong, but that is completely visual. Is there a tool in CCP4 that reports both spherical and ellipsoidal completeness (on merged reflection data)? That would make it easy to distinguish such cases.

Cheers,
Robbie



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Re: [ccp4bb] Completeness question

[Robbie Joosten]

Hi Ian,

> I don't see that anisotropic truncation has anything to do with the low
> spherical completeness as compared with the info in the co-ordinate file.
> Yes the spherical completeness after anisotropic truncation will be reduced,
> but why would it cause it to become inconsistent with that reported (unless
> of course the completeness calculations were performed on two different
> reflection files)?  Besides, the anisotropy is quite low (Delta-B eigenvalues:
> 3.42  -1.95 -1.47) so that couldn't explain it.
This is a general problem with anisotropic truncation. 6rjy is an example of 
something else going on. What happens is that people report the ellipsoidal 
completeness, but when you import the reflection data from the PDB and add the 
missing reflections (because those are typically not deposited) with the CCP4 
program complete you get a spherical dataset. If you now calculate the 
completeness it will be very low and inconsistent with the reported number. 
This is actually also a problem on the side of the PDB validation as EDS does a 
similar thing.

So what I want is a way to reproduce the reported completeness even when it is 
the ellipsoidal completeness. Not being able to do so would then be a clear 
indication that something else is going on like you see below. I suppose 
replacing complete with something that can add the missing ellipsoidal 
reflections would also solve the problem. If anything that would be even more 
elegant.

Cheers,
Robbie







> 
> I do agree that something has clearly gone wrong with the reflection
> deposition for 6RJY.  It could of course go right back to the collection or
> processing, but I think it unlikely anyone could solve the structure with data
> in this state!  Approximately alternate reflections are missing, but the
> pattern of absences does not correspond with any space group.  For example
> from MTZDUMP on the reflection file:
> 
>3   1   00.00 21.21  0.22
>3   1   20.00 23.83  0.19
>3   1   40.00 34.71  0.26
>3   1   60.00  9.06  0.11
>3   1   80.00 31.64  0.24
>3   1  100.00 31.22  0.25
>3   1  120.00  1.28  0.39
>3   1  140.00  6.59  0.12
>3   1  160.00 17.58  0.15
>3   1  180.00  3.94  0.18
>3   1  200.00 11.05  0.12
>3   1  220.00 34.24  0.24
>3   1  240.00 12.39  0.14
>3   1  260.00 12.76  0.15
>3   1  280.00 20.80  0.18
> 
>3   1  300.00 23.70  0.19
>3   1  320.00 23.47  0.20
>3   1  340.00 30.50  0.23
>3   1  360.00 10.93  0.22
>3   1  380.00 28.11  0.22
>3   1  400.00 24.41  0.21
>3   1  420.00 11.04  0.21
>3   1  440.00 12.58  0.28
>3   1  470.00 10.54  0.29
>3   1  490.00 10.54  0.23
>3   1  510.00  2.98  0.70
>3   1  530.00  5.84  0.39
>3   1  550.00  9.79  0.27
>3   1  570.00 11.33  0.26
>3   1  590.00  8.99  0.30
>3   1  610.00  1.84  0.76
>3   1  630.00  2.63  0.78
>3   1  650.00  4.91  0.46
>3   1  670.00  3.50  0.64
>3   1  690.00  1.93  0.76
>3   1  710.00  4.57  0.52
>3   1  730.00  1.71  0.73
> 
> 
> Note how the pattern switches between (3 1 44) and (3 1 47).
> 
> 
> So sometimes k+l = 2n are absent and sometimes k+l = 2n+1 are: this pattern
> pervades the whole dataset so the completeness (both spherical and
> ellipsoidal) is reduced by a factor of about two.  This makes no sense in
> terms of known systematic absences, and certainly not for the reported
> space group P212121.  This alternating pattern of absences is of course
> extremely unlikely in valid data: normally low completeness arises from
> whole missing wedges of data, or cusps, or to a smaller extent detector gaps,
> i.e. usually missing data are largely contiguous, not alternating as here.
> 
> 
> I think the only solution here is to get the authors to deposit the data
> correctly: is there any commonality of the authors for the structures where
> you have noted this problem?
> 
> 
> Cheers
> 
> 
> -- Ian
> 
> 
> 
> On Sat, 30 May 2020 at 09:36, Robbie Joosten
> mailto:robbie_joos...@hotmail.com> >
> wrote:
> 
> 
>   Hi Everyone,
> 
>   I've been looking at

[ccp4bb] Completeness question

[Robbie Joosten]

Hi Everyone,

I've been looking at some recent PDB entries that have much lower spherical) 
completeness than reported in the coordinate file. One reason for this is that 
the data were anisotropicly truncated, another reason is some mess-up with the 
deposition of the reflection data. There is a lot of discussion about the 
former practice and I don't want to go in to that, but the second one is 
obviously an error. Now how do I distinguish these cases?

Sometimes, you can look at the reported number of reflections and compare that 
to the deposited reflection file and you will find that something has clearly 
gone wrong. However, the reported number of reflections is not entirely 
reliable because of other issues so I'd rather not use it. If you use PDBpeep 
(e.g. for 6rjy) you can see something is wrong, but that is completely visual. 
Is there a tool in CCP4 that reports both spherical and ellipsoidal 
completeness (on merged reflection data)? That would make it easy to 
distinguish such cases.

Cheers,
Robbie



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Re: [ccp4bb] PDB file header lines...

[Robbie Joosten]

Hi Harry,

You need this: 
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL

Essentially you have to make sure a MODEL has a number and a closing tag. It is 
read as a real PDB record so you have to make sure it is correct BIDEN is not 
PDB compliant and will be either ignored or a parser will throw an error.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Harry
> Powell - CCP4BB
> Sent: Friday, May 29, 2020 16:57
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] PDB file header lines...
> 
> Hi
> 
> Is there something about “MODEL ” lines (i.e. five characters followed by a
> space) in PDB files that is completely beyond the pale?
> 
> I’ve got some PDB files from a protein structure prediction server based in
> the US that Coot fails to read and that cause QTMG to crash on my Mac. I’ve
> tracked this down to “MODEL” lines in the file headers.
> 
> I’ve tested this most in QTMG, so the following may not be true for Coot. If I
> change this line so that it has “M ”, “MO ”, “MOD ”, MODE ”, “MODEL1 ”,
> “MODEL22 ”, “MODEL678 ” or even “MODEL^&* ” instead of “MODEL ” then
> all looks hunky-dory.
> 
> I thought - “aha - there’s something about 5 characters” - so I tried 
> replacing
> “MODEL ” with “TRUMP ” and “BIDEN ” and the files read okay, so it does
> look very specific.
> 
> I’m sure there’s a simple answer to this (is there a “FM” I could read?), but 
> I
> haven’t found one yet. Can anyone on the BB help out?
> 
> Harry
> 
> ###
> #
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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Re: [ccp4bb] Fwd: Refmac error

[Robbie Joosten]

Hi Eugene,

We recently had this with a student as well and at least in PDB format the 
files are salvageable by doing a simple search and replace from , to .

Rather than going completely American, you can also just change the number 
format. In Windows 10 this is 
Settings > Time & Language > Data, time, & regional formatting (hidden on the 
right) > Additional data, time, & regional settings > Change data, time, or 
number formats > Additional settings

Only "decimal symbol" and "Digit grouping symbol" need to be set to . and , 
respectively. 

Cheers,
Robbie
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Eugene
> Krissinel
> Sent: Friday, May 29, 2020 12:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Fwd: Refmac error
> 
> Dear Nadine,
> 
> Many thanks for sharing your project with me on CCP4 Cloud. The reason for
> Refmac failure is absolutely clear: the previous Coot job exported PDB file,
> using commas (wie im besten Deutsch) instead of periods (as we would
> expect in best English) for all float-point numbers. You can see it if you go 
> to
> the previous Coot job report, scroll down to "Output Structure", press
> "Display" and scroll down a bit.
> 
> This effect is known to be peculiar to WinCoot -- have you used Windows
> machine to run Coot in job 179? And had you used a different machine to
> run Coot in job 169, which produced output file in correct format?
> 
> The only way to cope with the situation, known to me, is to ensure that your
> Windows machine uses US/English locale settings. This takes tweaking
> Language settings in Windows Control Panel and rebooting the machine.
> Regrettably, you will have to repeat job 179 in new locale. If it contains
> particularly valuable results that are difficult to reproduce, let me know 
> and I
> will advise you of the rescue procedure.
> 
> Admittedly, you are by far not the only one who encounters this problem,
> which appears in all locales with float point formats different from
> US/English. Therefore, I cc WinCoot developer on this email (they are aware
> anyway, and are working on the issue), as well as CCP4 BB list, where you
> placed your request initially, for other CCP4 users to be aware of this
> feature. And there is an obvious homework for us here at CCP4.
> 
> Once again, many thanks for your report. Please unshare this project now
> (simply remove my login name where you have put it for sharing before).
> 
> Kind regards,
> 
> Eugene
> 
> 
> On Fri, May 29, 2020 at 9:52 AM Nadine Gerlach   > wrote:
> 
> 
>   Hey Eugene,
> 
>   actually this happend not just for one project of mine, but I shared
> one project with you now. Scroll down to the last refmac run after model
> building with coot. I just tried it again but it is still the same result.
> 
>   Thanks for the help!!
> 
>   Nadine
> 
> 
> 
> 
> 
>   Am 28.05.2020 um 19:28 schrieb Eugene Krissinel:
> 
> 
>   Dear Nadine,
> 
>   We would need more information on what happens. You can
> share your project with me and I can have a look at it. To share the project,
> open it, then push Main Manu button in top-left corner, choose "Share" and
> set my login name (eugene), then confirm to me by e-mail. Your data and
> project will be treated as confidential.
> 
>   Many thanks for writing to us (use c...@ccp4.ac.uk
>   rather than BB list for this type of queries please)
> 
>   Eugene
> 
> 
>   -- Forwarded message -
>   From: Nadine Gerlach   >
>   Date: Thu, 28 May 2020 at 14:21
>   Subject: Refmac error
>   To: mailto:CCP4BB-
> requ...@jiscmail.ac.uk> >
> 
> 
> 
> 
>   Hey everybody,
> 
>   I am running refmac in CCP4 ccloud after Coot and I get this
> error message:
> 
>*** error running refmac5: Error in command.call
>   Return code: 512
> 
>   Any held is really appreaciated!
> 
>   Best wishes,
>   Nadine
>   --
>   Nadine Gerlach
>   PhD candidate
>   MPG MARUM Bridge Group Marine Glycobiology
>   MARUM, University Bremen & Max Planck Institute for
> Marine Microbiology
>   Tel: +49 421 218-65758
>   Email: nger­lach@mpi-bre­men.de  ,
> ngerl...@marum.de 
>   MARUM Pavillon room 1110
>   Leobener Straße
>   28359 Bremen, Germany
> 
>   This email and any attachments are intended solely for the
> use of the named recipients. If you are not the intended recipient you must
> not use, disclose, copy or distribute this email or any of its attachments and
> should notify the sender immediately and delete this email from your
> system. UK Research and Innovation (UKRI) has taken 

Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)

[Robbie Joosten]

> On 26/04/2020 16:21, Abhishek Anan wrote:
> > Dear all,
> >
> > I have a peptide crystal structure at 0.97 Å that contains two surface
> > exposed Methionine. The CE atoms of both MET have a suspiciously high
> > b-factor >40 and a positive density. In addition, the sulfur atom SD
> > has a large negative density (b-factor ~23).
> >
> > I initially suspected that the MET may have oxidized to MET-sulfoxide
> > and tried to model only the MET-sulfoxide. This again resulted in
> > negative density.
> >
> > I think that the peptides might be partly oxidized which brings me to
> > my question. Is there a way to model both MET and MET-sulfoxide into
> > the density much like alternate conformation with options to refine
> > their respective occupancies.
> 
> 
> Yes. This is called micro-heterogeneity
> 
> And is documented here:
> 
> https://www.wwpdb.org/documentation/procedure
> 
> That should "just work" if you then give the model to refmac.
> 
> FWIW, Coot is, AFAIR, not 100% happy with such models.
Neither is Refmac ☹

Cheers,
Robbie


> 
> Paul.
> 
> 
> 
> 
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Re: [ccp4bb] Ligand discrimination

[Robbie Joosten]

Hi Nicolas,

VHELIBS does a good job at that. Keep in mind though that the distinction 
between additives and functional molecules is done based on a list of 
compounds. There are compounds that can serve both as crystallisation agent and 
ligand in different contexts.

Cheers,
Robbie 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Nicolas
> Soler
> Sent: Friday, March 27, 2020 13:28
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Ligand discrimination
> 
> Dear all,
> 
> Could somebody point me to a good tool that providing a pdb id, could
> analyze its ligand(s) and distinguish between crystallographic agents and
> putative drugs.
> 
> Many thanks in advance,
> 
> Nicolas
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Hydrogens in PDB File

[Robbie Joosten]

Hi Dale,

You make very valid points and there are good reasons to keep the refined 
hydrogen positions (methyl twists an protonation of HIS are good examples). 
There is a way of distinguishing refined a modelled hydrogens in mmCIF and we 
should start using that.
About protonation of hustidines: WHAT IF does quite a decent job although there 
is room for improvement around ligands.
About maps from EDS: These were (and perhaps are) made by running 0 cycles of 
unrestrained refinement in Refmac. Unrestrained refinement takes away the need 
to sort out restraints which was an absolute nightmare at the time. A 
side-effect of unrestrained refinement is that Refmac cannot (could not) add 
hydrogens. PDB-REDO needs restraints anyway so this does 0 cycles restrained 
refinement to generate the first maps and adds hydrogens in the process. This 
addition is not that sophisticated, but it should make the maps better. Have a 
look https://pdb-redo.eu/db/3eoj.zip

Cheers,
Robbie

On 1 Mar 2020 09:26, Dale Tronrud  wrote:

Dear Ethan,

   To move away from an abstract discussion of hydrogen atoms I'd like
to describe a concrete example.  In 2008 I deposited a model of the FMO
(Bacteriochlorophyll containing) protein.  The ID code is 3EOJ.  The
model was refined to a data set cut off at 1.3 A resolution using the
criteria of the day.  I used shelxl for the final stage of refinement
and added riding hydrogen atoms to the mix.  When I deposited the model
I succumb to peer pressure and removed the hydrogen atoms.

   If you look at the map calculate by the Electron Density Server you
will see many peaks in the Fo-Fc map indicating the missing hydrogen
atoms.  (I have attached a screen-shot from Coot but I recommend that
you fire up Coot and explore the map yourself.)  In my picture you can
see the three peaks around a methyl group.  Above and to the left is the
peak for the hydrogen of a CH bridging atom in the Bacteriochlorophyll-a
ring.  To the right and in the distance is a peak for the hydrogen of a
CH2 group.  Not every hydrogen is represented by a positive peak, but
they exist throughout the map.  This Fo-Fc map is useless for the
purpose of assessing the quality of my model, since the true residuals
are hidden among all these hydrogen peaks.

   A critic might say that these peaks are simply the result of the
model being biased toward the presence of hydrogen atoms and therefore
an artifact.  A model refined to this data set w/o hydrogen atoms would
not likely show peaks indicating that hydrogen atoms need to be built.

   I would say that the map calculated from a Hydrogen-free model is the
biased one.  I am 99% confident in the location of most of the riding
hydrogen atoms and leaving them out results in a model that is
fantastically unlikely.  The absence of peaks in an apo map is a flaw in
that map.  I would describe it as "vacuum bias".  "Biasing" a model
toward reality is not a problem.

   This example shows that the current PDB is incompatible with models
whose Hydrogen atoms have been stripped.  To get proper maps and
validation reports one has to either preserve the Hydrogen atoms in the
model, or modify all the software that uses coordinate files to add the
hydrogen atoms back in.  That is a major programming task, which the
authors have, apparently, been unwilling to do.

   I will go further and disagree with you that even this is a solution.
It is very difficult to add the Hydrogen atoms back into 3EOJ, and I
expect this difficulty is the reason software has not been written that
successfully does it.

   There are two major problems to be overcome in 3EOJ.  shelxl has an
option to twirl the methyl groups and select the torsion angle with the
best fit to the map.  The hydrogen atoms in the pictured methyl group
weren't built as staggered -- All values for the torsion angle were
tested and it happens that the best fit placed them in a staggered
conformation.  That is a much more interesting result.  There are other
methyl groups around the edges of the Bchl-a molecules that are crowded
and the methyl groups are observed to have torsion angles that are not
standard for riding Hydrogen atoms.  The neighboring methyl groups avoid
H-H bumps by twisting and that twist can be detected by shelxl in the
1.3 A data.

   The second problem is the matter of Histidine residues.  There are
two Nitrogen atoms in the side chain.  A hydrogen atom could be on
either one, and sometimes both have hydrogens.  A very clever program
could work out from the hydrogen bonding pattern the most likely
placement, but I've not seen any program that is very good with hydrogen
bonding networks.  Worst still, I've often seen programs place the
hydrogen atom *between* the Nitrogen and Magnesium atoms of a Histidine
ligand to a Bacteriochlorophyll a.  This mistake will certainly lead to
very bad geometry!

   Until an hydrogenation program is written that can handle all
ligands, all hydrogen bonding networks (even overlapping 

Re: [ccp4bb] What resolution - X-ray diffraction round this time

[Robbie Joosten]

Hi Dusan,

I don't know what the correct answer is but I think it is safe to see that your 
referee has outdated views (trying to stay polite here). I/sigI > 2.0 with 
decent completeness would be not be seen as to agressive by most (but as too 
conservative by others!). From that cut-off you could push the resolution to 
I/sigI > 1.0 by paired refinement and still be safe because you show there is 
useful information in the data.

One thing I do notice that there are still quite a lot of people overstressing 
the resolution in their manuscripts. This causes a lot of unnecessary 
discussion with referees. It is not a well established number, so don't make a 
big deal of it if the point of the paper is about biology rather than methods.

Cheers,
Robbie

On 28 Feb 2020 09:22, dusan turk  wrote:

Hi,

Browsing through the recent discussion on EM data resolution cutoff it occurred 
to me that the X-ray diffraction community isn’t that unanimous either.

My stand:

When the default resolution cutoff provided with the data processing software 
in electron density map calculation and refinement delivers quality maps 
noisier than expected and/or too high R-factors I start adjusting the 
resolution cutoff by lowering the resolution and trying alternative space 
group.   Hence, I allow the data processing programs to suggest where to draw 
the line (be it CC1/2, I/sigI, R merge, R sym, R p.i.m. and R r.i.m, …) , 
unless there are problems.

Doing so, I came into a dispute with a referee who shaped his request:

"It is well accepted that the criteria for resolution cutoff should consider 
both I/SigI and Rmerge for the outer most shell. For data sets collected at 
synchrotron sources, the criteria of I/SigI > 5 and Rmerge <50% can be taken as 
a good practical reference.”

So where do we stand? Which are the most objective criteria for resolution 
cutoff to be used in diffraction data processing? Which number of shells to use 
when calculating the statistics? Do we have a consensus?

best wishes,

dusan turk



Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biology
fax:  +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com



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Re: [ccp4bb] disulfides in coot

[Robbie Joosten]

Hi Sam,

Once a disulfide bridge is made Coot will restrain the sulfur atoms to bind. 
The way out is deleting one of the side chains and adding it back while making 
sure the sulfurs do not get too close.

HTH,
Robbie

On 18 Feb 2020 11:24, Sam Tang  wrote:
Dear all

A very technical question which I believe a few simple mouse clicks would 
solve. Is there a way I can ask Coot not to build the disulfide linkage 
automatically (which lies within a strong red density)?

My WinCoot is version 0.8.9.2

Many thanks!

Regards

Sam



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Re: [ccp4bb] Refmac5 question

[Robbie Joosten]

Hi Joern,

The logic behind it this is that those are hydrogen position that are uncertain 
due to possible flips and free rotation (tyr, thr, ser). You should probably 
only set these occupancies to 1.00 after you have studies the local hydrogen 
bonding network.

Cheers,
Robbie 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Joern
> Krausze
> Sent: Tuesday, February 4, 2020 10:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac5 question
> 
> Dear all,
> 
> I've got a Refmac5 question. When I refine my protein structure in Refmac5
> with the options make hydrogen ALL and make hout yes, some of the
> hydrogen atoms in the output file have zero occupancies. At a first glance,
> only the the H-atoms attached to OG1 of Ser, ND2 of Asn, and NE2 of Gln are
> affected. These hydrogen atoms were present in the input file with their
> occupancies matching that of the residues they are attached to. Is there a
> reason for this behavior that I might be missing? I am currently running
> Refmac version 5.8.025.
> 
> 
> 
> 
> Best regards,
> 
> Joern
> 
> 
> --
> *
> Address:
> 
> Joern Krausze
> Department of Plant Biology
> Braunschweig University of Technology
> Spielmannstr. 7
> 38106 Braunschweig
> Germany
> 
> Email:  j.krau...@tu-braunschweig.de  braunschweig.de>
> Phone:  +49 (0)531 3915858
> *
> 
> 
> 
> 
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Re: [ccp4bb] Remember the turkey?

[Robbie Joosten]

If there is a better term because the current one is incorrect or unsuitable, 
I'm all for changing it. We changed GRID to AIDS (the name was factually wrong) 
and the names of quarks were also changed in the history of particle physics 
(because we found better terms). At the same time we still use somewhat 
derogatory terms in astrophysics (e.g. MACHO and WIMP) and in the olden days 
IDE drives still had masters and slaves and we still have loads of silly names 
(remember TWAIN?).

However, quantum advantage and quantum supremacy mean different things and 
should not be mixed. In this context it is a good term as it describes the 
state at which quantum computing can do something regular computing cannot. 
This is in stark contrast with the (anti)social use of supremacy which is 
AFAICT always factually wrong. Here, the authors make an issue (I believe out 
of virtue signaling) without coming with an adequate solution. I do not find 
that constructive at all.

Cheers,
Robbie

On 2 Jan 2020 08:29, Frank Von Delft  wrote:

Those authors raise a fair point though, don't they:  if nothing else,
"suppremacy" is an utterly daft word to use in any scientific context,
since it brings nothing technical to the table.

Before geek triumphalism became the rage (or maybe before the need for
grant-gaining hyperbole?), we might have selected adjectival phrases by
referring to style guides like Strunk and White, which consistently
emphasise informative simplicity.  But when companies get to call
themselves "Uber" without being pilloried for it I guess we know those
days are long gone.

phx.



On 26/12/2019 18:46, Bernhard Rupp wrote:
> Hi Fellows - here some light Holiday entertainment (and puzzle) for you:
>
> Remember my thanksgiving posting below?  Meant as  a hoax or satire, it 
> follows the
> classical pattern of throwing postmodern Critical Theory gibberish and Social 
> Justice key words
>   (successfully deployed by Alan Sokal)
> https://en.wikipedia.org/wiki/Sokal_affair
> onto an out-of-context situation with the purpose of virtue signaling and 
> posturing on moral high ground.
>
>   Well, we just got outdone by a letter in our favorite vanity magazine, 
> Nature:
> https://www.nature.com/articles/d41586-019-03781-0
>
> The parallels are fascinating and it exactly follows the recipe developed 
> above:
> " throwing postmodern Critical Theory gibberish and Social Justice key words 
> onto an out-of-context situation
> with the purpose to signal virtue and to opportunity for posturing on moral 
> high ground"
>
> Now - is this comment (a) meant serious or (b) another successful 
> Sokal-Turkey-type hoax?
>
> Cheers, BR
>
> --
> It has come to our attention that on this bulletin board insensitive and 
> hurtful comments have
> been made towards animals with disability. Particularly concerning is the 
> display of white privilege
> and racial bias towards a minority individual  given that the turkey is also 
> referred to in German as 'Indian'.
> In view of this non-inclusive and divisive display of unwokeness, the faculty 
> Bias Response Team
> will contact you shortly and allow you to present your self-critique.
>
> We want this board to remain a safe zone inclusive of all animals, complete 
> or not.
>
> Stuffed, BR
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Jurgen Bosch
> Sent: Thursday, November 28, 2019 13:51
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
>
> Think of completeness with an analogy to turkey.
> Say you happen to find a one-legged turkey (incomplete by conventional 
> standard) you could still stuff it and put it in the oven and enjoy 93% of 
> the turkey. The 7% missing, who cares? Other than I like both legs of the 
> turkey :-)
>
> Happy Thanksgiving everyone
>
> Jürgen
>
> 
>
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Re: [ccp4bb] technical question

[Robbie Joosten]

Or use the residue name MHO if SME has the wrong hand around the sulfur.

Cheers,
Robbie

On 29 Nov 2019 21:47, Paul Emsley  wrote:

On 29/11/2019 18:06, amit gaur wrote:

> I want to replace a particular methionine in a pdbwith methionine sulfoxide( 
> an oxidized form of
> methionine). Can body please tell me how to do this? I am familiar with 
> pymol, chimera and coot software.

In Coot:

Extensions -> Modelling -> Replace Residue -> SME -> Mutate



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Re: [ccp4bb] TLS parameters

[Robbie Joosten]

Hi Eleanor,

The blocks are reliably recorded in PDB entries but in some cases the 
renumbering of residues was not pushed through to TLS groups. Certain 
selections cannot be captured in the PDB format, for instance the split in main 
chain and side chain that Refmac allows. Fortunately that feature is hardly 
used.
Parsing TLS records is not straightforward, particularly the sets from Buster 
suffered a lot from inconsistent manual editing in the early days of TLS 
refinement. PDB-REDO's extractor does a decent job in getting selections and 
changing those into Refmac format, but there are definitely cases that it 
cannot do. We also have a tool that does this for mmCIF files which is not 
written by me and (therefore) much more sophisticated in handling more 
complicated cases. 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Eleanor
> Dodson
> Sent: Tuesday, November 19, 2019 3:59 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] TLS parameters
> 
> Does anyone know how reliably the different programs record and use these
> blocks from the PDB file?
> 
> Eleanor
> 
> 
> 
> 
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Re: [ccp4bb] why does Coot ignore CONECT?

[Robbie Joosten]

Hi Paul,

I think this is a very good call as CONECT records are notoriously unreliable. 
Many PDB files don't have them and many programs don't update them when you 
change atom numbers. Even in annotated PDB entries there are many problems with 
those. It's better to forget about them altogether and focus on the mmCIF 
format.

Cheers,
Robbie

On 2 Nov 2019 02:15, Paul Emsley  wrote:

On 01/11/2019 20:17, Pavel Mader wrote:
> Hello,

Hello.

>
> I have a question, can anyone explain, why does Coot not display a covalent 
> bond manually specified by
> CONECT line in a pdb file?

Because I have never thought them necessary. Using SSBOND, LINK and residue 
dictionaries seemed to me to
cover the bases for which CONECT would be used.

Paul.



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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Robbie Joosten]

Hi Chris,

You made an Fobs map not a 2Fo-Fc map. You can leave sigma empty if you want to 
make a map in this case.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Chris Fage
> Sent: Monday, September 30, 2019 14:00
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol
> 
> Dear Paul, Herman, Robbie, and Santosh,
> 
> Thanks for your quick replies.
> 
> The FFT-generated maps and mtz maps look roughly equivalent in Coot, but
> there are minor differences even at the same e/A^3 level (the mtz maps
> actually look a bit weaker). I generated them using the default settings in
> FFT: simple map, format to cover asymmetric unit, F1=F_XDSdataset,
> Sigma=SIGF_XDSdataset, PHI=PHIC. Perhaps, as Robbie mentioned, the
> problem lies in column selection, since Coot uses FWT and PHWT. I can assign
> F1 and PHI to these values, respectively, but what should I choose for Sigma?
> 
> My version of Pymol doesn't support loading of mtz files. I think it's only in
> the incentive version.
> 
> Paul wrote: "No need to do this - just export the map (or the map
> fragment)." I'm not sure how to do this without going through FFT!
> 
> I can also try generating maps in Phenix, as Santosh suggested. However, if
> the maps can be directly exported, as Paul suggested, I would prefer to
> follow that route.
> 
> Best wishes,
> Chris
> 
> 
> 
> 
>   signature?utm_medium=email_source=link_campaign=sig-
> email_content=webmail> Virus-free. www.avg.com
>  signature?utm_medium=email_source=link_campaign=sig-
> email_content=webmail>
> 
> 
> On Mon, Sep 30, 2019 at 12:49 PM Santhosh Gatreddi
>  wrote:
> 
> 
>   Hi Chris,
> 
>   I also observed similar thing when I have generated 2Fo-Fc maps in
> CCP4 FFT. But when I have generated 2Fo-Fc maps in Phenix then my maps
> were similar  in Pymol and Coot. I request you to generate maps with Phenix
> and verify it in Pymol. It worked for me.
> 
>   One possible reason for this is map averaging in Pymol. Make sure
> that you uncheck it before loading your map in Pymol.
> 
>   I hope that above suggestion works for you.
> 
>   Regards,
>   Santhosh
> 
>   On Mon, Sep 30, 2019 at 4:06 PM Chris Fage 
> wrote:
> 
> 
>   Dear All,
> 
>   I recently obtained structures of a protein bound to two
> different small molecules. When viewing the structures in Coot with a similar
> contour setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than
> that around ligand 2.However, after generating 2Fo-Fc maps in FFT and
> loading them in Pymol (again, choosing equal contour levels), the maps
> surrounding ligands 1 and 2 have nearly the same quality. Is there a
> difference in scaling between the two programs that can account for this?
> Thanks for any advice!
> 
>   Best wishes,
>   Chris
> 
>   signature?utm_medium=email_source=link_campaign=sig-
> email_content=webmail> Virus-free. www.avg.com
>  signature?utm_medium=email_source=link_campaign=sig-
> email_content=webmail>
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-
> bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
>   --
> 
>   With regards
> 
>   Santhosh Gatreddi (Research Scholar)
>   c/o Dr.Insaf Ahmed Qureshi,
>   Dept. of Biotechnology & Bioinformatics,
>   School of lifesciences,
>   University of Hyderabad,
>   Hyderabad-500046(A.P),
>   India.
>   Ph.no-9160628684.
> 
> 
> 
> 
> 
> 
> 
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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Robbie Joosten]

Are you sure you used the right columns in FFT? AFAIK Coot uses FWT and PHWT.

I thought the more recent PyMOL versions finally had MTZ support, or is this 
just for the incentive version? Also if it is for looking at the structure and 
making figures, perhaps try  CCP4mg. It has proper MTZ support and it is of 
course much better integrated with CCP4. It also is boss-proof for figures, 
i.e. it puts a recovery file next to the figure so you can go back quickly to 
change the carbon colours to a more mauve-y shade of pinky russet. 

Cheers,
Robbie



> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Chris Fage
> Sent: Monday, September 30, 2019 12:37
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol
> 
> Dear All,
> 
> I recently obtained structures of a protein bound to two different small
> molecules. When viewing the structures in Coot with a similar contour
> setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than that
> around ligand 2.However, after generating 2Fo-Fc maps in FFT and loading
> them in Pymol (again, choosing equal contour levels), the maps surrounding
> ligands 1 and 2 have nearly the same quality. Is there a difference in scaling
> between the two programs that can account for this? Thanks for any advice!
> 
> Best wishes,
> Chris
> 
>   signature?utm_medium=email_source=link_campaign=sig-
> email_content=webmail> Virus-free. www.avg.com
>  signature?utm_medium=email_source=link_campaign=sig-
> email_content=webmail>
> 
> 
> 
> 
> 
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Re: [ccp4bb] What OS do you use?

[Robbie Joosten]

Since the answers are open, the analysis will involve a lot of curation. I'm 
interested in the final results.

Cheers,
Robbie

On 22 Sep 2019 04:45, Murpholino Peligro  wrote:
I want to know what operating system you use.
For that I made a poll, it is anonymous, quite simple and plus you get to see 
the results.
(link https://forms.gle/7VT4pgbHQQmeAvpp8)
I hope you contribute.

Thanks




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Re: [ccp4bb] Rfree from another mtz file

[Robbie Joosten]

I totally agree. And because the new dataset is of higher resolution, there 
will be new reflections in the test set anyway.

Now if you want to use the same testset always for series of isomorphous 
datasets (even though you do not need to), you can do this:
- Use unique to make a full set of reflections given your space group and cell 
dimensions
- Assign a testset to that file using the program freerflag
Foreach dataset:
- Copy over the testset from you master file
End

Note that the testsets in the datasets will be super/subsets of each other but 
assuming the data are complete they will be the same if you use the same 
resolution cut-offs.

Cheers,
Robbie

On 17 Sep 2019 02:17, Tim Gruene  wrote:

Dear Mariana,

you can simply create a new set for Rfree, independently of the previous one.
It will be as good as the copied one, and there is no reason why you would
need to maintain the same flags. As Ian Tickle explained only briefly ago,
your new data set will have new, independent errors.

Best regards,
Tim

On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote:
> Dear all,
>
> We tried to use the Rfree set from a lower resolution data with a higher
> resolution from the same Crystal. To do so We used aimless at ccp4i with
> the option use free flag from another mtz file and extend the data.
>
> I think it worked, but now we don't know how to be sure we have the same
> Rfree set. Does anyone have a way to prove it?
> Thank you in advance,
> Best,
> Mariana
>
> 
>
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--
--
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] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

[Robbie Joosten]

Well, it's not exactly normal. We could use some extra information...
Exactly the same, or just very similar? Are the values high or low? Is it a 
viral capsid?

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tung Thanh Dinh
> Sent: Friday, August 30, 2019 15:37
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-
> work and r-free values are equal?
> 
> After phasing with phenix, i clicked on the phenix.refine ribbon. Since then
> for every macrocycle of refinement, r-work and r-free values are always the
> same. Is this a problem that I need to fix?
> 
> 
> 
> 
> 
> Kindest regards,
> Tung Dinh
> 
> PhD student
> The University of Georgia
> Department of Chemistry
> 
> 
> 
> 
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