Re: [ccp4bb] Lower b-factors with increasing T

[Ethan A Merritt]

On Wed, Sep 7, 2022 at 11:57 AM Matt McLeod  wrote:

> Hi everyone,
>
> I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A),
> 313K (2.2A) and I am curious as to the details in determining B-factors.
>



In the larger physical universe those temperatures are not very far apart.
I would not expect much change in the physical properties of the crystal
or its content.There is a reason that "cryo" crystallography generally
means "liquid nitrogen temperature", i.e. 77K but more like 100K at the
position of a crystal in a boil-off nitrogen stream.

The first thing you should check when comparing B factors is whether the
different refinements use the same, or closely comparable, overall
B correction.  Typically this is an anisotropic correction; you would
want to add an isotropic approximation of this overall term to the
individual refined atomic B factors and then compare the sums.
That gives you a back-of-the-envelope comparison.

To do a more thorough job is complicated.

I am of course highly biased towards the power of TLS 
My suggestion would be to first use the refined B factors you have to
construct a segmented TLS model. I would then reset all the Bs to a
constant and refine the data sets in parallel using a "pure TLS" model,
i.e. no individual atomic B factors.
Afterward I would compare the magnitude of the principle components
of each TLS segment as a function of the data collection temperature.
The rationale is that the individual TLS segments are chunks of the
structure, domains, subdomains, loops, etc, that may be relatively
free to vibrate within the crystal lattice.  You would expect the
magnitude of this vibration to increase with temperature.
Not so much the individual atomic vibrations described by atomic
B factors.

Ethan


> I have treated these datasets more-or-less identically for comparison's
> sake.  I used DIALS to index, integrate, and scale the data.  I scaled the
> data to a ~0.6 CC1/2 cutoff.
>
> After fully refining the datasets, there is an odd trend with respect to
> temperature (from what has been previously published) and I assume that
> this is because of "behind-the-scenes" computation rather than a
> biophysical observation.  The B-factors slightly decrease from 252-293K,
> and then significantly drop at 313K.  The maps look pretty well identical
> across the datasets.
>
> 253K - 53.8 A^2
> 273K - 48.4 A^2
> 293K - 45.5 A^2
> 313K - 18.6 A^2
>
> I compared the wilson intensity plots from DIALS scaling for 273K and 313K
> and they are very comparable.
>
> I am looking for suggestions as to where to look at how these b-factors
> are selected or how to validate that these B-factor are or are not
> accurate.  Also, any relevant literature would be welcomed.  From what I
> have read, there is a general trend that as T increase, the atoms have more
> thermal energy which raises the b-factors and this trend is universal when
> comparing datasets from different temperatures.
>
> Thank you and happy to supply more information if that is helpful,
> Matt
>
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] MR solution not working

[Ethan A Merritt]

On Wednesday, 2 March 2022 20:43:42 PST Shubhashish Chakraborty wrote:
> Hello,
> I am trying to solve a dataset using molecular replacement. However, neither 
> Phaser MR nor Molrep can give any solution. 
> In Phaser, I have received an advisory that Top FTF has not packed. 
> I have tried molecular replacement using the wild-type protein at different 
> resolutions (I am working on a mutant).
> Also, I have truncated the loops from the input structure. However, none have 
> worked. 
> So, what can be the possible way to solve this data set?

Double check your space group.
Then check it again.
If there is any chance you integrated the data in the wrong space
group, go back and process it again with lower symmetry.

Break the model into domains; feed phaser the individual domains for
separate placement.

good luck

Ethan


>  
> Thank you
>  
> Shubhashish Chakraborty
> PhD JRF 2018
> Structural and Molecular Biology Lab (Varma Lab)
> Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
> Khargar, Navi Mumbai
> E-mail: schakrabo...@actrec.gov.in
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] interesting map problem

[Ethan A Merritt]

On Friday, 17 December 2021 14:04:17 PST Christine Gee wrote:
> Hi,
> 
> I recently came across this strange issue. I was using aimless in CCP4 to
> scale my data and apply an Rfree from a reference .mtz
> 
> Neither the reference or the file I was working with had higher resolution
> than 1.5
> However aimless wrote out h, k, l and Rfree to 0.4. I did not click the
> button to extend resolution by the way.
> 
> No big deal right? Well Coot then assumed the resolution was 0.4 and wrote
> out maps to super high resolution and everything took forever to render,
> making coot basically unuseable.

Coot->File
->Open mtz
select mtz file by name
->Expert Mode
->Use Resolution Limits
set high resolution limit to 1.5

However, I would worry that the spurious resolution is symptom of
a more pervasive problem.

Ethan


> 
> I could not find any global or local parameter in coot that seemed to
> remedy this.
> 
> Did anyone come across anything similar? What is the solution besides
> editing the resolution of the .mtz file output from aimless and what
> program woud you recommend for this?
> 
> My simple solution for now was to use an .mtz file output from aimless that
> a reference Rfree was not applied to.
> 
> Regards
> Christine
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] A strange problem related to MR

[Ethan A Merritt]

Two questions

(1) What is the rotation+translation operation that relates
solution #1 an solution #2? 

(2) Have you double-checked and then checked yet again that both
solutions are in P43212?  Could it be that one of them ended
up in, say, P414241?

it's happened to me :-(   
Ethan


On Sunday, 5 September 2021 21:45:39 PDT Lande Fu wrote:
> Dear all,
> 
> 
> Recently I had a strange problem related to MR and it confused me and my 
> colleagues a lot. 
> 
> My protein crystal was diffracted at 2.63A and I processed it normally then 
> did MR with Phaser (in P432(1)2). The result itself looked okay and well fit 
> the map. However, the R-work/ R-free value was stuck at 0.3012/0.2434 after 
> cycles of manual refinement. Then I redid MR with another model from PDB 
> website and got another solution which looked similar to previous one and the 
> R-work/ R-free value can be lowered to 0.2496/0.1967 after refinement. 
> 
> Strange things appeared when I opened the two MR solutions in single coot 
> window (Fig 1). The two models were neither overlaying each other nor on the 
> symmetry of the other. The two models are nearly identical (actually the 
> first model was a previous structure built from PDB model) and have same 
> construct with my protein. There is no TNCS, twinning or other noticeable 
> problems detected according to aimless log. 
> 
> My question is: why phaser gives two different solutions from same map and 
> similar model and result in different R-work/ R-free value? Does that mean 
> there are two phases in the map? Does that imply multiple lattices in my 
> crystal?  
> 
> I tried to research myself but did not find any related explanation for it. 
> Please let me know if you need more information. Thank you in ahead.
> 
> 
> Regards,
> 
> Lande Fu


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] biomolecular NMR for IDPs

[Ethan A Merritt]

It is possible that you could address some of your questions
more quickly and much more cheaply by small-angle scattering,
either light (SAS) or X-ray (SAXS).

I would suggest looking into those avenues first.

If you have well behaved (i.e. non-aggregating) purified proein
and access to synchrotron beam time (easily requested),
a series of SAXS experiments could probably be conducted in one day.
I don't want to oversell SAXS, I'm not really an enthusiast.
But this case, categorizing the interaction of two poorly ordered proteins
in solution and in particular the facilitation or disruption of this
interaction by small molecules, should be well within its scope.

best

Ethan

On Saturday, 14 August 2021 14:12:40 PDT Sorin Draga wrote:
> Hello everyone,
> 
> I do realize that this is not a NMR focused group, but I do hope that there
> are a few spectroscopists lurking around that could possibly answer a few
> questions (I am more of a modeler/computationalist):
> 
> The problem: I have two intrinsically disordered proteins that are known to
> interact (let's call them 1 and 2). I would like to get structural
> information (a conformational ensemble) for 1 and for the "complex" (1+2).
> Further down the line (depending on whether this is possible) I would also
> like to evaluate potential small molecule inhibitors for the said complex.
> Both 1 and 2 are <200 aminoacids long.
> 
> The questions:
> 
> 1. Could the cost of determining the "structure" for 1 and 1+2 be
> estimated? To be more precise, I am looking for a ball-park figure on how
> much a NMR measurement would cost in this case.
> 2. Could anyone recommend a good group/CRO that could provide such a
> service and not have an astronomical cost?
> 3. Any other suggestions/thoughts that you think might be worth mentioning
> (minimum quantity of protein necessary, purity, type of NMR etc)
> 
> Many thanks for your help and time!
> 
> Cheers!
> 
> Sorin
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Meaning of a pdb entry

[Ethan A Merritt]

On Monday, 31 May 2021 10:53:46 PDT Gergely Katona wrote:
> Dear Ethan,
> 
> Thank you for your comments! I started a new thread, it was unfortunate that 
> I brought this up in a discussion about B-factors. I really wanted to discuss 
> something that is model agnostic and how to represent uncertainty by 
> sampling. I consider an ensemble model with multiple partial occupancy 
> molecules is still one model. 

Gergely,

Your questions touch on topics that are far too broad to address
satisfactorily on the bulletin board.  I will offer a few thoughts.

- The PDB format has supposedly been deprecated in favor of mmcif,
but let's disregard that.

- A PDB file can contain any number of models. Each is introduced
by a record with "MODEL " in columns 1-6.  The documentation said
  "The MODEL record specifies the model serial number when multiple
   structures are presented in a single coordinate entry, as is often
   the case with structures determined by NMR."
Note that it mentions NMR as an example but does not limit use
of multiple model sections to NMR experiments.

- The PDB format allows [requires?] a header record with with
"EXPDTA" in columns 1-6.  This is used to identify whether the 
model coordinates in the file are supported by X-ray data, NMR data,
theoretical calculation, fiber diffraction, etc.
I don't know how long the list grew to be.

In the context of your question, this EXPDTA information is important.
For example my earlier comment that ensemble models are not
statistically justified was specifically with regard to modeling
X-ray crystal diffraction data.  Generating an ensemble to describe,
say, snapshots of an MD simulation is an entirely different story.

- "Uncertainly" is pretty vague.
Just sticking with crystal structures, it could mean.

1) This is definitely the mean position for this atom in this
crystal but there is uncertainty in how much individual instances
in different crystal unit cells within the lattice deviate from
this mean.

2) This is a best-effort description of the position of a ligand
atom.  However it is uncertain what fraction of the unit cells
contain the ligand at this position, or at all.

3) It is likely that this sidechain/loop/subunit is present in
different conformations in different copies of the unit cell.

4) The coordinates of this specific atom/residue/conformation
are well supported by the data for this particular crystal.
But it might be somewhere else in the next crystal from the
same crystallization drop, or in a crystal from a different
crystallization buffer, or at another temperature, or in
solution, or in the presence of a ligand, etc.
 
best

Ethan


> I am not sure if it is possible to use MODEL-ENDMDL loops in pdb or mmcif 
> format for storing multiple crystallographic models. I assume it is already 
> possible to store multiple structure factor files (for refinement, for 
> phasing, different crystals etc) under the same entry. In my mind, it would 
> be a small step to associate different data sets distinguished by crystal ID 
> or data block with a particular model number, but maybe it is not that 
> simple. 
> 
> I do not want to create multiple pdb entries just to provide evidence for the 
> robustness/reproducibility of crystals and crystallographic models. I would 
> rather use different pdb entries for different sampling intentions: for 
> example entry 1 contains all the control crystals, entry 2 contains all the 
> crystals subjected to treatment A, etc. These would otherwise share identical 
> data reduction and refinement protocols and most of the metadata. I am afraid 
> I do know how the PDB and associated services work internally, but I hope 
> someone here can provide guidance.
> 
> Best wishes,
> 
> Gergely
> 
> 
> Gergely Katona, Professor, Chairman of the Chemistry Program Council
> Department of Chemistry and Molecular Biology, University of Gothenburg
> Box 462, 40530 Göteborg, Sweden
> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
> Web: http://katonalab.eu, Email: gergely.kat...@gu.se
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ethan A Merritt
> Sent: 29 May, 2021 19:16
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS
> 
> On Saturday, 29 May 2021 02:12:16 PDT Gergely Katona wrote:
> [...snip...]
>  I think the assumption of independent variations per atoms is too strong in 
> many cases and does not give an accurate picture of uncertainty.
> [...snip...]
> 
> 
> Gergely, you are revisiting a line of thought that historically led to the 
> introduction of more global treatments of atomic displacement.
> These have distinct statistical and interpretational advantages.
> 
> Several approaches have been tried

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Ethan A Merritt]

s, analogously how MD 
> trajectories can be described as average structures and covariance matrices.  
> I think the assumption of independent variations per atoms is too strong in 
> many cases and does not give an accurate picture of uncertainty.
> 
> Best wishes,
> 
> Gergely
> 
> Gergely Katona, Professor, Chairman of the Chemistry Program Council
> Department of Chemistry and Molecular Biology, University of Gothenburg
> Box 462, 40530 Göteborg, Sweden
> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
> Web: http://katonalab.eu, Email: gergely.kat...@gu.se
> 
> From: CCP4 bulletin board  On Behalf Of Hughes, 
> Jonathan
> Sent: 28 May, 2021 14:49
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS
> 
> hi ian,
> yes, that aspect was in my mind, a bit, but i wanted to keep it simple. my 
> point wasn't really how the "uncertainty" parameter is derived but rather its 
> units. i can imagine that uncertainty in 3D could be expressed in ų (without 
> helping the naïve user much) or in Å (which to me at least seems useful), but 
> Ų (i.e. the B factor) seems neither logical nor helpful in this context, 
> irrespective of its utility elsewhere. if you just see the B factor as a 
> number, ok, you can do the √ in your head, but if it's visualized as in 
> pymol/putty larger uncertainties become exaggerated – which is another word 
> for "misrepresented".
> cheers
> j
> 
> Von: Ian Tickle mailto:ianj...@gmail.com>>
> Gesendet: Freitag, 28. Mai 2021 12:10
> An: Hughes, Jonathan 
> mailto:jon.hug...@bot3.bio.uni-giessen.de>>
> Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS
> 
> 
> Hi Jonathan
> 
> On Thu, 27 May 2021 at 18:34, Hughes, Jonathan 
> mailto:jon.hug...@bot3.bio.uni-giessen.de>>
>  wrote:
> 
>  "B = 8π2  where u is the r.m.s. displacement of a scattering center, and 
> <...> denotes time averaging"
> 
> Neither of those statements is necessarily correct: u is the _instantaneous_ 
> displacement which of course is constantly changing (on a timescale of the 
> order of femtoseconds) and cannot be measured.  So u2 is the squared 
> instantaneous displacement,   is the mean-squared displacement, and so 
> the root-mean-squared displacement (which of course is amenable to 
> measurement) is sqrt(), not the same thing at all as u.
> 
> Incidentally, the 8π2 constant factor comes from Fourier-transforming the 
> Debye-Waller factor expression I mentioned earlier.
> 
> Also for crystals at least, the averaging is not only over time, it's over 
> all unit cells, i.e. the displacements are not only thermal in origin but 
> also due to spatial static disorder (instantaneous differences between unit 
> cells).
> 
> 
> it would seem to me that we would be able to interpret things MUCH more 
> easily with u rather than anything derived from u².
> So then I think what you mean is sqrt() rather than , which seems not 
> unreasonable.
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

[Ethan A Merritt]

Well, since you ask...

I prefer, and recommend, Mageia.  Second choice SuSE.

I find that the default configuration and choice of packages on these
are a better fit to my use in development and computation both on my
lab machines/servers and on my desktop/laptop. 

cheers,
Ethan

On Friday, 19 February 2021 12:35:46 PST 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-stream/
> 
> 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&A=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/
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

[Ethan A Merritt]

It may be here already.

For a value of B that includes "no worse than the starting point",
the so-called "UK variant" currently spreading in the US meets your
criteria.  Some projections show it displacing other potentially
more dangerous variants while not not degrading the impact of 
vaccination and other public health measures.

Are you starting a conspiracy theory that it was the result of
a clandestine good samaritan molecular biologist?

Ethan

On Wednesday, 17 February 2021 12:39:21 PST Jacob Keller wrote:
> I was under the impression that A,B,C are not strongly or intrinsically
> coupled, for one, since there are so many varieties of viruses with so much
> range of infectiousness and clinical severity. False impression?
> 
> B + C = vaccine
> 
> A + B + C = immunosysadmin pandemic updater virus. Patient 0 honors given
> for each (yearly?) edition to curry political favor.
> 
> JPK
> 
> 
> On Wed, Feb 17, 2021 at 3:03 PM Tim Gruene  wrote:
> 
> > Hi Jacob,
> >
> > how do you think this should be possible? In order to infect others,
> > the virus particle needs to proliferate (that's the only thing it
> > does). It profilerates by hijacking the machinery of one cell of your
> > body and turn it into a virus factory. Your body does not like this
> > abuse and kills the cell, and also tries to kill the virus particles.
> > The virus does not make you sick, it only captures one cell. The
> > reaction of your body to kick out the virus, and the cell that does not
> > do it's job anymore, make you sick. A and B are mutually exclusive. B +
> > C is named vaccine.
> >
> > Best,
> > Tim
> >
> >
> > On Wed, 17 Feb 2021 12:33:09 -0500 Jacob Keller
> >  wrote:
> >
> > > It would seem to me that it should be possible to generate versions
> > > of the Covid virus that would:
> > >
> > > A. be extremely contagious and yet
> > > B. be clinically benign, and
> > > C. confer immunity to the original covid virus.
> > >
> > > If, then, this virus could be released, with appropriate "kill switch"
> > > safeguards built in, would this not solve the world's pandemic
> > > problems? Is there any reason, practically, why this approach would
> > > not be feasible?
> > >
> > > Maybe we don't really know enough to manipulate A, B, C yet?
> > >
> > > Or maybe it's too scary for primetime...nightmare bio-warfare
> > > apocalypse?
> > >
> > > Has this sort of thing been done, or does it have a name?
> > >
> > > Jacob
> >
> >
> >
> > --
> > --
> > 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
> >
> 
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Data 3 A

[Ethan A Merritt]

On Tuesday, 12 January 2021 15:22:18 PST rohit kumar wrote:
> Dear all,
> 
> I am trying to solve a data with 3 A resolution, however data quality is
> very bad and mathews coffi. suggest  two molecules per ASU but It always
> gives one molecule in AU after phaser with the TFZ and RFZ score are 4.5
> and 3.5 respectively with LLG gain 121.
> And when I used that model for Refmac the final R/Rfee is 23/30 and with
> satisfactory Ramachandran statistics as well as electron density and model
> in agreement with each other  in coot. Does It mean that I have
> correct solution?

Sounds promising.
The other to check is that the model you have exhibits a set of lattice
contacts sufficient to form a believable crystal packing.  If the 
symmetry-related
molecules do not touch each other then there must be some component
missing from your model.

cheers,

            Ethan


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] possible solution with Phaser

[Ethan A Merritt]

On Tuesday, 5 January 2021 23:38:02 PST Luca Mazzei wrote:
> Hi all,

The generic answer is to make another Phaser run using the three good
placements as a known substructure and searching for a single copy of
the monomer.  Since it might be minor collisions that are causing a
bad translation score, you could relax the acceptance criteria for clashes.

The more interesting answer might be to inspect a difference map
made from the three good placements only.   My past experience with
such cases is that the missing copy is often apparent by eye and
you can place it manually in Coot by dragging the whole molecule
as a rigid group into the difference density.  Not perfectly, but
close enough to get the rest of the way with rigid body refinement.

This step may also reveal an obvious clash with one or more of the
three previous placements that is due to flexible loop you could
cut out and rebuild later.

good luck and best wishes for the New Year,

Ethan


> 
> I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff strongly 
> suggests the presence of 4 mol per asym unit (space group P6222). The results 
> after a search of 4 mol per asymmetric unit of my monomer are the following:
> 
> ** SINGLE solution
> 
> ** Solution written to SOL file:  phaser_3f6v_A1_MOLREP.sol
> 
> ** Solution written to PDB file:  phaser_3f6v_A1_MOLREP.1.pdb
> ** Solution written to MTZ file:  phaser_3f6v_A1_MOLREP.1.mtz
>Solution annotation (history):
>SOLU SET  RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0 PAK=3 
> LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7)
> LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5 
> LLG=795 TFZ==5.4
>SOLU SPAC P 62 2 2
>SOLU 6DIM ENSE autoMR EULER  125.3   60.8  300.2 FRAC  0.17 -0.13  0.08 
> BFAC -9.34 #TFZ==10.0
>SOLU 6DIM ENSE autoMR EULER  305.4   60.8  300.2 FRAC  0.27 -0.16  0.08 
> BFAC -5.29 #TFZ==29.8
>SOLU 6DIM ENSE autoMR EULER  294.7  119.1  120.3 FRAC  0.45  0.01  0.26 
> BFAC  0.34 #TFZ==22.5
>SOLU 6DIM ENSE autoMR EULER  305.5   61.6  300.1 FRAC  0.11 -0.16  0.08 
> BFAC 29.19 #TFZ==5.4
>SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD  0.93 #VRMS  0.79
> 
> It seems (also looking at the maps) that it correctly places three monomers 
> out of four. How can I use this information to improve the search of the 
> fourth monomer using the same template model?
> 
> Thanks in advance for your help,
> 
> Best regards
> 
> Luca Mazzei
> 
> Luca Mazzei - PhD
> Laboratory of Bioinorganic Chemistry
> Department of Pharmacy and Biotechnology (FaBiT)
> Alma Mater Studiorum - University of Bologna
> Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy
> Tel: +39 0512096235
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] over-fitting? over-refinement?

[Ethan A Merritt]

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 in model refinement.

You can find a copy of the paper on my web site:

E.A. Merritt (2012). "To B or not to B: a question of resolution?" 
Acta Cryst. D68, 468-477.
http://skuld.bmsc.washington.edu/~tlsmd/ActaD_68_468.pdf

cheers,

Ethan
> 
> BRS
> 
> Sam

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Best protocols to advance a low resolution twin

[Ethan A Merritt]

n to find.
> 
> 
> 
> 
> 
> I realise I can go two ways, either using the detwinned data or using twinned 
> data and supplying the operator.the former giving ridiculously optimistic 
> R-values with a suspiciously "clean map", the latter giving noisier but maybe 
> more informative maps.
> 
> 
> 
> 
> 
> Two-fold averaging is not going to be great because the d2-d3 arrangement 
> observed in monomer 1 clashes when placed over monomer 2 (so at present can 
> only average the small % of ASU between d3 copies). Critically, looking for a 
> second d2 using MR fails but the lack of crystal contacts suggests success 
> should be possibleits really unlikely that a third entity is in there (d1 
> and d2 are actually 50% similar, so by searching for d2 and failing, I'm 
> actually missing three spots it could potentially occupy if the protein is 
> not proteolysed)
> 
> 
> 
> 
> 
> Sorry for long email but the devil is in the details. My question would be, 
> what is best practice in a low res poor twinned dataset where you can only 
> fill roughly just over half of what should be in there?
> 
> 
> 
> 
> 
> Feel free to tell me its doomed!
> 
> 
> 
> 
> 
> Best wishes & thanks in advance
> 
> 
> Andy
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
>  https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>   
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
>   
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] polarizer

[Ethan A Merritt]

On Sunday, 16 August 2020 12:14:59 PDT Diana Tomchick wrote:
> If only glass is placed between the polarizer and analyzer, the crystal will 
> not show artificial colors (try it in a 9-well Pyrex depression plate). The 
> artificial colors come from the diffraction of visible light from the plastic 
> ware, which depending upon the type of plastic and the way the plate is 
> manufactured, will have some preferred orientation of the polymer chains. 
> Although it could have more to do with the method of manufacture of the plate.
> 
> I would love to hear a different explanation from someone that either sells 
> or manufactures crystallization plastic ware.

The question was about using a circular polarizer, which has two components,
a linear polarizing component and a quarter wave plate.

A pair of circular polarizers with a crystal between them will have the same
primary effect as a pair of linear polarizers.  But the "quarter wave plate" is
by its nature wavelength dependent.  So you get selective removal/transmission
of different color components.

Ethan


> 
> Diana
> 
> **
> Diana R. Tomchick
> Department of Biophysics, Rm. ND10.214A
> University of Texas Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Dallas, TX 75061 USA
> 214-645-6383 (office)
> 
> On Aug 16, 2020, at 12:19 PM, Nukri Sanishvili  wrote:
> 
> 
> EXTERNAL MAIL
> 
> Hi All,
> 
> Adding some more details to what's been said already. Only because I've seen 
> too many times the polarizers being used incorrectly.
> First, you need two polarization filters which are typically called polarizer 
> and analyzer. First one (the polarizer) lets through only the light waves of 
> a certain polarization. Then one needs to rotate the other one (analyzer) 
> until there is no more light getting through. At this point the analyzer 
> blocks the light that was let through by the polarizer This is what Diane 
> referred to as 90 degrees. Please note that the polarizer-analyzer plates 
> stay parallel to each other. After that, a crystal is placed between them and 
> is rotated. Unless it is a crystal with cubic symmetry, at some angles it 
> will light up in beautiful colors and at some angles it will not. This is 
> because the crystal changes the polarization of the light passing through and 
> "90 degree setup" of the polarizer/analyzer pair is no longer valid for newly 
> polarized light.
> Please note that using plastic plates in this context is not quite 
> appropriate. The plastic polymer itself changes the polarization as well and 
> therefore it breaks the main principle of this method. With plastic 
> interference, it will be impossible to reach complete darkening of the field 
> of view. I can almost hear a lot of people saying that they've used it with 
> plastic plates without a problem. I believe it to be the case but it still 
> doesn't make it right.
> Best,
> Nukri
> 
> On Sun, Aug 16, 2020 at 9:15 AM Matthias Zeug 
> mailto:matthias.z...@gmx.de>> wrote:
> Hi all,
> 
> The polarizer-microscope in our facility is not working properly, and I have 
> to check my plates using a standard stereo-microscope. As a workaround, I 
> thought about buying one at Amazon, placing it on top of the plates and 
> rotating it to still test for birefringence.
> 
> The product is linked below. Does anyone have some experience with this kind 
> of "homemade" system? And also (this might be a stupid question), does the 
> product even work? As far as I know, the polarizers in the microscopes are 
> linear polarizers, whereas the product linked below is a circular polarizer. 
> I would also be happy for product recommendations (optimally available at the 
> German Amazon).
> 
> Cheers
> 
> Matthias
> 
> https://www.amazon.de/dp/B00XNMXYBY/ref=cm_sw_r_cp_apa_i_5YsoFbFQXTBP9
> 
> ___
> Buchmann Institute of Molecular Life Sciences
> Goethe University Frankfurt
> 
> 
> 
> UT Southwestern
> 
> Medical Center
> 
> The future of medicine, today.
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Ethan A Merritt]

On Wednesday, 1 July 2020 18:50:57 PDT Jose Brandao-Neto wrote:
> Hi Ian, good to hear! Hi everyone, thanks for the etymological - and 
> etiological - discussion. I'm good whatever the choice.
> 
> John, I beg to differ with the absolute statement that xfels offer damage 
> free hkls - back in 2016 yet another great experimental work, by Inoue et al 
> (https://www.pnas.org/content/113/6/1492), showed global loss of diffraction 
> in a protein crystal analog as soon as 10 fs from exposure start (later 
> estimated in Mx experiments by I. Schlichting's team).

That's the "destroy" part of "diffract and destroy".

Since an XFEL pulse can be shorter than 10 fs,
that observation does not contradict the idea that the measured
diffraction occurs faster than the damage.

Ethan

> Cheers,
> José

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Strange Pseudosymmetry Effects

[Ethan A Merritt]

On Wednesday, 27 May 2020 18:49:23 PDT Jessica Bruhn wrote:
> Hello,
> 
> I am wondering if pseudosymmetry can cause weak reflections that mimic the
> doubling of one unit cell axis' length. Has anyone seen something like this
> before?

Yes.

>  I am processing data from a small molecule sample collected with electron
> diffraction from multiple crystals. For the b axis, it is not clear if the
> length should be 10A or 20A. There are spots with the correct spacing for
> b=20A, but every other spot seems weaker than the spots along k if I choose
> b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data. I
> have solved this structure in P1 with b=10 and found four molecules in the
> ASU and in P212121 with b=10 resulting in one molecule in the ASU. 

> In P1, three of the four molecules adopt the same conformation, but the fourth
> molecule is in an alternate conformation that causes only ~1/2 of the
> molecule to be consistent with the first three. In P212121 I see density
> for part of this alternative conformation, but the full molecule in this
> alternate conformation cannot pack properly in P212121. Based on these
> results and some orthogonal data, I think I should refine the solution in
> P1 with b=10. Does it seem reasonable that pseudosymmetry is causing these
> weak reflections along k hinting at a doubling of the b axis?

This description makes me think also of a supercell.  This can happen
when, say, the position of one copy N is not compatible with all (N-1) of
the others positions.  Some unit cells contain (N-1) copies but not the
problematic N; other cells contain the N copy but miss one or more of
the others to make room.  This gives you a stochastic mix of cell
contents.  If it were truly random you'd see spots for a small cell
but the contents would have to be described by partially occupied sites.
But if there is a bias towards alternation of cells +N -N +N -N you
get a pseudo-doubling of that cell edge, matching your description.

Suggested reading:
Lovelace J, Petrícek V, Murshudov G, Borgstahl GEO.
Supercell refinement: a cautionary tale. Acta Crystallogr D Struct Biol. 2019 
Sep 1;75(Pt 9):852-860. 
doi: 10.1107/S2059798319011082. Epub 2019 Aug 28. PMID: 31478908; PMCID: 
PMC6719663.

I've had to deal with these in macromolecular crystals.
I would imagine that the same can happen for electron diffraction
but I can't point to any prior examples in the literature.

good luck!

        Ethan

> Thanks in advance!
> 
> Best,
> Jessica
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] What refinement programs are fully Open Source?

[Ethan A Merritt]

On Thursday, 7 May 2020 13:58:55 PDT David Waterman wrote:
> Dear Ethan,
> 
> The copy of xia2 that I have on my machine says at the top of the source
> > # Copyright (C) 2013 David Waterman
> > #
> > # This code is distributed under the terms and conditions of the
> > # CCP4 Program Suite Licence Agreement as a CCP4 Application.
> 
> 
> This surprised me greatly. I wondered if perhaps you were referring to the
> ccp4i2 GUI for xia2, for which I must admit responsibility. However, I
> can't find "Copyright (C) 2013 David Waterman" anywhere within the current
> release of CCP4, so I am perplexed.

I sincerely apologize for inferring more than I should have from that snippet.
My search may indeed have picked up a wrapper rather than the program
itself.  Here is what I did:

head `locate bin/xia2`

> I would like to make it clear that xia2 is not distributed under the terms
> of the CCP4 licence. It has a permissive free software licence, namely
> BSD-3, which must surely conform to any reasonable definition of Open
> Source. See here https://github.com/xia2/xia2/blob/master/LICENSE
> 
> While xia2 has certain modes that run non-open software, Graeme's point is
> that the default mode runs DIALS, which is BSD-3 as well.
>
> -- David

The larger point was that xia2 is not so much a computational code by
itself as an open-ended framework for multiple codes that are not
uniformly licensed or available for code inspection/modification.
I hope I have that right!  

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] What refinement programs are fully Open Source?

[Ethan A Merritt]

On Thursday, 7 May 2020 10:18:38 PDT Roversi, Pietro (Dr.) wrote:
> Thank you Ethan for taking the the time to answer and explain.
> Yes I am sure I have asked a vague and imprecise question.
> 
> Practically, I am going to point to xia2 for data processing:
> https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Xia2/manual.html
> 
> and hope it is "Open Source enough" - without too much scrutiny on 
> dependencies?

I may misundertand the full scope of xia2, but I believe it is a scripted 
pipeline
that invokes other programs.  Those other programs individually may have
their own very different licensing or distribution or use restrictions.
The user guide you linked to says
if you use xia2 in published work please include the references 
for the programs it has used, which are printed at the end of the
output.

The copy of xia2 that I have on my machine says at the top of the source

# Copyright (C) 2013 David Waterman
#
# This code is distributed under the terms and conditions of the
# CCP4 Program Suite Licence Agreement as a CCP4 Application.

So I guess the first question is whether the CCP4 License Agreement
meets your definition of Open Source.

The next question would be what programs did xia2 choose to run?
Some of these may meet your criteria for Open Source, others not.
For example, does xia2 invoke shelx?  Does shelx meet your criteria?

Ethan



> 
> So, what about a refinement suite of programs that is "just as Open Source" 
> as xia2 is for data processing?
> 
> Unless this second message of mine is making my re-drafted question worse 
> than the original one 🙂.
> 
> with best wishes,
> 
> Pietro
> 
> 
> Pietro Roversi
> 
> Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/
> 
> LISCB Wellcome Trust ISSF Fellow
> 
> <https://bit.ly/2I4Wm5Z>https://le.ac.uk/liscb/research-groups/pietro-roversi
> 
> 
> Leicester Institute of Structural and Chemical Biology
> Department of Molecular and Cell Biology, University of Leicester
> Henry Wellcome Building
> Lancaster Road, Leicester, LE1 7HB
> England, United Kingdom
> 
> Skype: roversipietro
> Mobile phone  +44 (0) 7927952047
> Tel. +44 (0)116 2297237
> 
> 
> 
> 
> From: Ethan A Merritt 
> Sent: 07 May 2020 18:08
> To: Roversi, Pietro (Dr.) 
> Cc: CCP4BB@jiscmail.ac.uk 
> Subject: Re: [ccp4bb] What refinement programs are fully Open Source?
> 
> On Thursday, 7 May 2020 09:34:13 PDT Roversi, Pietro (Dr.) wrote:
> > Dear all,
> >
> > we are in the editorial stages of a manuscript that I submitted to Wellcome 
> > Open Research for publication.
> >
> > The journal/editor ask us to list fully Open Source alternatives to the 
> > pieces of software we used, for example for data processing and refinement.
> >
> > What refinement programs are fully Open Source?
> 
> There are recurring battles and philosophical fractures over what exactly
> "open source" means, either in practice or aspirationally.
> You would do well to provide a definition before asking people for
> suggestions that meet your criteria.
> 
> At one point the Open Source Foundation (OSF) claimed to have the authority
> to declare something was or was not "open source" and kept lists of
> approved code, but their definition was in conflict with guidelines from
> other places including funding agencies [*].  Also the OSF itself seems to
> have largely disappeared from view, so maybe that's a bad place to start.
> 
> There are at least two fracture lines in this battle.
> The one created by people who feel a need to distinguish between
> "free/libre code" and "open code",  and the one created by people
> whose main concern is "documentation and claims are not enough;
> I need to see the code actually used for the calculations reported in
> this work".
> Then there's the concern mostly of interest to corporate legal
> departments "can we use this in our commercial products".
> 
> Ethan (coding veteran with scars from this battle)
> 
> 
> [*] it was also in conflict with the ordinary English language meaning
> of "open" and "source", which didn't help any.
> 
> 
> >
> > Thanks!
> >
> > Pietro
> >
> >
> > Pietro Roversi
> >
> > Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/
> >
> > LISCB Wellcome Trust ISSF Fellow
> >
> > <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbit.ly%2F2I4Wm5Z&data=02%7C01%7Cpr159%40leicester.ac.uk%7Cf8cc2fb23bb84707d7a708d7f2a96338%7Caebecd6a31d44b01

Re: [ccp4bb] What refinement programs are fully Open Source?

[Ethan A Merritt]

On Thursday, 7 May 2020 09:34:13 PDT Roversi, Pietro (Dr.) wrote:
> Dear all,
> 
> we are in the editorial stages of a manuscript that I submitted to Wellcome 
> Open Research for publication.
> 
> The journal/editor ask us to list fully Open Source alternatives to the 
> pieces of software we used, for example for data processing and refinement.
> 
> What refinement programs are fully Open Source?

There are recurring battles and philosophical fractures over what exactly
"open source" means, either in practice or aspirationally.
You would do well to provide a definition before asking people for
suggestions that meet your criteria.  

At one point the Open Source Foundation (OSF) claimed to have the authority
to declare something was or was not "open source" and kept lists of 
approved code, but their definition was in conflict with guidelines from
other places including funding agencies [*].  Also the OSF itself seems to
have largely disappeared from view, so maybe that's a bad place to start.

There are at least two fracture lines in this battle.
The one created by people who feel a need to distinguish between
"free/libre code" and "open code",  and the one created by people
whose main concern is "documentation and claims are not enough;
I need to see the code actually used for the calculations reported in 
this work".
Then there's the concern mostly of interest to corporate legal
departments "can we use this in our commercial products".

Ethan (coding veteran with scars from this battle)


[*] it was also in conflict with the ordinary English language meaning
of "open" and "source", which didn't help any.


> 
> Thanks!
> 
> Pietro
> 
> 
> Pietro Roversi
> 
> Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/
> 
> LISCB Wellcome Trust ISSF Fellow
> 
> <https://bit.ly/2I4Wm5Z>https://le.ac.uk/liscb/research-groups/pietro-roversi
> 
> 
> Leicester Institute of Structural and Chemical Biology
> Department of Molecular and Cell Biology, University of Leicester
> Henry Wellcome Building
> Lancaster Road, Leicester, LE1 7HB
> England, United Kingdom
> 
> Skype: roversipietro
> Mobile phone  +44 (0) 7927952047
> Tel. +44 (0)116 2297237
> 
> 
> 
> ############
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] disinfecting keyboards

[Ethan A Merritt]

On Wednesday, 29 April 2020 11:53:32 PDT Tim Gruene wrote:
> Dear all,
> 
> can you make suggestions for how to disinfect computer keyboards, and
> instrument panels?

The consensus here is that the keyboards must have a cover that can be
washed/disinfected.  They are not [usually] that hard to find. Sometimes
they are called "skins" rather than covers.

Instrument panels - no idea.  Labs here have discussed instituting a strict
tagging system with a log.  One user per instrument, separated by
[72 hours? not sure if there is a consensus] between users. 

Ethan

> 
> Our facility is going to reboot next week, with shifts so that people
> don't meet. The main interface will be the computer keyboards, as well
> as the door of our X-ray diffractometer and the mounting of the
> crystals.
> 
> The keyboard labels may not like alcohols (and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
> 
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
> 
> But maybe there are other ways that won't require gloves?
> 
> Best regards,
> Tim
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Average B factors with TLS

[Ethan A Merritt]

On Tuesday, 7 April 2020 05:16:58 PDT Nicholas Keep wrote:
> I am at the point of depositing a low resolution (3.15 A) structure 
> refined with REFMAC.  The average B factors were 31 before I added the 
> TLS contribution as required for deposition which raised them to 157- 
> this is flagged as a problem with the deposition, although this did not 
> stop submssion.  The estimated Wilson B factor is 80.5 (although that 
> will be quite uncertain) so somewhere between these two extremes.

While this is a larger discrepancy that I would have expected,
you may find a partial explanation in Merritt [2011]

  "Some B eq are more equivalent than others"
  Acta Cryst. (2011). A67, 512–516

This is part of why I have always opposed expanding TLS models
into ANISOU records for deposition.  

> Is it only the relative B factors of the chains that is at all 
> informative?  Should I report the rather low values without TLS 
> contribution or the rather high ones in any "Table 1"?  Comments 
> appreciated.

I would replace the "Biso" values in your deposition with
recalculated "Beq", explain this in the remarks, and tell the
deposition facilitator that you take responsibility for your
model as deposited.

But first I would recheck everything in the process, because
that really does sound like a larger than expected change.

Note: I have succeeded in depositing without the "required"
ANISOU records, although only after several rounds of discussion.

     good luck,

Ethan


> 
> Thanks
> 
> Nick
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] [3dem] Which resolution?

[Ethan A Merritt]

On Sunday, 8 March 2020 01:08:32 PDT Rangana Warshamanage wrote:
> "The best estimate we have of the "true" B factor is the model B factors
> we get at the end of refinement, once everything is converged, after we
> have done all the building we can.  It is this "true B factor" that is a
> property of the data, not the model, "
> 
> If this is the case, why can't we use model B factors to validate our
> structure? I know some people are skeptical about this approach because B
> factors are refinable parameters.
> 
> Rangana

It is not clear to me exactly what you are asking.

B factors _should_ be validated, precisely because they are refined parameters
that are part of your model.   Where have you seen skepticism?

Maybe you thinking of the frequent question "should the averaged refined B
equal the Wilson B reported by data processing?".  That discussion usual
wanders off into explanations of why the Wilson B estimate is or is not
reliable, what "average B" actually means, and so on.  For me the bottom
line is that comparison of Bavg to the estimated Wilson B is an extremely
weak validation test.  There are many better tests for model quality.

Ethan



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Hydrogens in PDB File

[Ethan A Merritt]

Matthew:

I think your nice summary leaves out an important point that has not been
explicitly mentioned.  That is the question of whether depositing hydrogens
actually adds information to the model. I submit that for a typical protein
refinement it does not.  The model is adequately described by saying
"hydrogens were added in their riding positions". This, together with 
knowledge of the refinement program used, is sufficient to reconstruct
the full model.  

This is an example of a recurring concern of mine that model validation
should include consideration of whether the model is overly complex.
Unless you have an abundance of data (which admittedly your 1.0Å case
might) there are insufficient observations to refine 3 positional parameters
for each hydrogen as if they were free variables.  We typically bypass this
by instead using the riding hydrogen model, which adds effectively a single 
on/off parameter for the entire mode (plus a small number of implicit
parameters that describe the ideal riding geometry, but those are 
normally taken as a priori knowledge rather than free variables).

So I find deposition of hydrogens for a typical resolution structure to
be more misleading than useful.  The correct, parsimonious, description is the
one-line statement that a riding hydrogen model was used.

It is tangential to your question, but I hold the same view about depositing
ANISOU records for a structure when the source of the anisotropy is solely
a TLS model, either with or without individual Biso contributions.
The parsimonious description is to give the TLS parameters and the Biso
component, if any.   These can be expanded to regenerate per-atom
ANISOU parameters if desired by a downstream program.  
If you deposit ANISOU records it implies that the Uij terms they describe
are free variables, but they are not.  (or anyway IMHO they should not be,
although PHENIX can violate this stricture).

My view is that for a typical structure (i.e. worse than say 1Å resolution data)
depositing hydrogen positions and ANISOU records at best does no harm. 
Unfortunately it implies a statistically unjustifiable model treatment.
The justifiable model is adequately described by the small number of
parameters in the header records;  the hydrogen coordinates and ANISOU
parameters are redundant dross.  

I fully understand that your original question was driven by cases where
you do have very high resolution data and so the statistical justification of
refining individual hydrogens or anisotropic ADPs enters a different realm.

Ethan


On Friday, 28 February 2020 20:22:17 PST Whitley, Matthew J wrote:
> Dear all,
> 
> I want to thank everyone who responded to my query about whether or not to
> include hydrogens in PDB depositions when they were explicitly included in
> the model during refinement.  In addition to the replies posted to this
> bulletin board, I received numerous replies sent directly to my email
> address.
> 
> To clarify one more time for casual readers so that we are all on the same
> page: because these two structures happen to be at high resolution (1.0 and
> 1.2 Å, respectively), I decided to include explicit hydrogens in the model
> for refinement, as recommended by the documentation for both Phenix and
> Buster, which I used for these refinements.  For the Phenix refinements,
> hydrogens were added by phenix.ready_set, whereas for the Buster
> refinements the hydrogenate tool was used.  My understanding is that both
> of these eventually call the reduce tool from MolProbity.  Unsurprisingly,
> the presence of hydrogens on the model led to both better model geometry
> and lower R-factors, although at these resolutions there is no observable
> density for the vast majority of the H-atoms in any of the refined maps.
> 
> Because the presence of the hydrogens improved the model, I have decided to
> leave the hydrogens at their refined positions for deposition.
> 
> I do want to point out one thing for readers interested in this topic: based
> on all the replies I received, there are a number of differing opinions
> (and therefore different practices) as to whether hydrogens should be
> included in deposited structures.  The expressed opinions ranged from the
> ethical (if the hydrogens were there for refinement, then it’s only fair
> that they be present in the deposited structure so that downstream users
> know what went into generating the reported statistics) to the practical
> (if the paper’s conclusions don’t rely on any arguments based on hydrogen
> atom positions, then there’s no compelling reason for them to be there;
> include them or don’t, it doesn’t matter.)  Because opinions seem to vary,
> perhaps it would be worthwhile for the PDB to issue some guidance on the
> matter for the future.
> 
> Have a nice weekend, everyone.
> 
> Matthew
> 
> ---
> Matthew J. Whitley, Ph.D.
> Research Instructor
> Department of Pharmacology & Chemical Biology
> University of Pittsburgh School of Medicine

Re: [ccp4bb] Hydrogens in PDB File

[Ethan A Merritt]

On Friday, 28 February 2020 11:19:37 PST Diana Tomchick wrote:
> If you deposit an mmCIF file that contains both the observed and calculated
> structure factors from your final round of refinement, then the PDB
> auto-validation reports the same (or so close to the same as to be
> negligible) R factors.

Yes, that's the "Depositor" line in the validation report.
The separate "DCC" line tries to recalculate from the model description.
It matches quite well if your model matches its default expectations,
but otherwise it can diverge.  It's a useful check that you haven't made
some inadvertent mistake in preparing the deposition files, but beyond
that it is less useful than, say, confirming that the model refinement
can be reproduced by feeding it to PDB-Redo.

Ethan


 
> Phenix outputs all of this automatically for you if you click the correct
> radio button in the GUI.
 
> 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<mailto:diana.tomch...@utsouthwestern.edu>
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
> 
> On Feb 28, 2020, at 12:51 PM, Ethan A Merritt
> mailto:merr...@uw.edu>> wrote:
 
> EXTERNAL MAIL
> 
> On Thursday, 27 February 2020 16:34:50 PST Alexander Aleshin wrote:
> Ethan wrote:
>- If you are not making claims about hydrogens but just want to
> describe what you did during refinement, I'd go with taking them out
> 
> I've noticed that REFMAC and Phenix use riding hydrogens to calculate the
> refinement statistics, and their exclusion affects R/Rfree. As a result, it
> is not clear what values should be reported.
> 
> In my opinion, riding
> hydrogens play same role as the TLS parameters, which we keep in a pdb
> submission. So, I am not convinced their omission is a good idea.
> I think PDB curators should provide a guidance  how to deal with issues
> like
 a resolution of anisotropic or incomplete data sets, riding
> hydrogens, sequence numbering etc.
> 
> Alex:
> 
> You are right that the PDB auto-validation step of recalculating R factors
> from the deposited model and observed F's is far from perfect.
> I have not looked at the DCC source code, but my impression from the
> R factors it spits back at me during deposition:
> - it ignores TLS records
> - it ignores the header record specifying choice of solvent model
> - it does use scattering factors f' and f" from the mmcif coordinate file
> - I have no idea what it does with twinning descriptions
> 
> As a result there is often a noticeable discrepancy between the R-factors
> from "Depositor" and "DCC" in the validation reports.
> 
> Regards,
> Alex
> 
> 
> 
> 
> On 2/27/20, 4:05 PM, "CCP4 bulletin board on behalf of Ethan A Merritt"
> mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of
> merr...@uw.edu<mailto:merr...@uw.edu>> wrote:
 
>[EXTERNAL EMAIL]
> 
>On Thursday, 27 February 2020 15:35:05 PST Whitley, Matthew J wrote:
> 
> Hello all,
> 
> 
> 
> I am nearly finished refining the structures of two mutant proteins
> from
> crystals that diffracted to very high resolution, 1 Å and 1.2 Å,
> respectively.  Refinement was conducted in the presence of explicit
> hydrogens on the models.  I am preparing to deposit these models into
> the
> PDB but am unsure about whether to retain or remove the hydrogens for
> deposition.  On one hand, these hydrogens were explicitly used during
> refinement, so that makes me want to keep them, but on the other hand,
> they
> were added at theoretical positions by MolProbity’s reduce tool
> for refinement and were not positioned on the basis of experimentally
> observed electron density, so that makes me want to delete them from
> the
> experimental model.  Which is the preferred option for this
> situation?
> 
> 
>The order of operations you describe is unclear.
> 
>If you explicitly refined hydrogens then their final positions are
> indeed
> based on experimentally determined data.
>The fact that you initially placed them into ideal geometry is not
> really
> any different from the non-H atoms of individual protein residues
> in your model, whose original positions were also based on known
> stereochemistry.
>On the other hand, if you mean that the hydrogens you used for
> refinement
> were deleted and replaced during validation by Molprobity
> (which I think it may do by default) that's not good.  You should rather
> keep th

Re: [ccp4bb] Hydrogens in PDB File

[Ethan A Merritt]

On Thursday, 27 February 2020 16:34:50 PST Alexander Aleshin wrote:
> Ethan wrote:
> - If you are not making claims about hydrogens but just want to
> describe what you did during refinement, I'd go with taking them out
> 
> I've noticed that REFMAC and Phenix use riding hydrogens to calculate the
> refinement statistics, and their exclusion affects R/Rfree. As a result, it
> is not clear what values should be reported. 

> In my opinion, riding
> hydrogens play same role as the TLS parameters, which we keep in a pdb
> submission. So, I am not convinced their omission is a good idea. 
> I think PDB curators should provide a guidance  how to deal with issues like
> a resolution of anisotropic or incomplete data sets, riding hydrogens,
> sequence numbering etc. 

Alex:

You are right that the PDB auto-validation step of recalculating R factors
from the deposited model and observed F's is far from perfect.
I have not looked at the DCC source code, but my impression from the 
R factors it spits back at me during deposition:
- it ignores TLS records
- it ignores the header record specifying choice of solvent model
- it does use scattering factors f' and f" from the mmcif coordinate file
- I have no idea what it does with twinning descriptions

As a result there is often a noticeable discrepancy between the R-factors
from "Depositor" and "DCC" in the validation reports.
 
> Regards,
> Alex 
> 
>   
> 
> 
> On 2/27/20, 4:05 PM, "CCP4 bulletin board on behalf of Ethan A Merritt"
>  wrote:
 
> [EXTERNAL EMAIL]
> 
> On Thursday, 27 February 2020 15:35:05 PST Whitley, Matthew J wrote:
> 
> > Hello all,
> >
> >
> >
> > I am nearly finished refining the structures of two mutant proteins
> > from
> > crystals that diffracted to very high resolution, 1 Å and 1.2 Å,
> > respectively.  Refinement was conducted in the presence of explicit
> > hydrogens on the models.  I am preparing to deposit these models into
> > the
> > PDB but am unsure about whether to retain or remove the hydrogens for
> > deposition.  On one hand, these hydrogens were explicitly used during
> > refinement, so that makes me want to keep them, but on the other hand,
> > they
 were added at theoretical positions by MolProbity’s reduce tool
> > for refinement and were not positioned on the basis of experimentally
> > observed electron density, so that makes me want to delete them from
> > the
> > experimental model.  Which is the preferred option for this
> > situation?
> 
> 
> The order of operations you describe is unclear.
> 
> If you explicitly refined hydrogens then their final positions are
> indeed
 based on experimentally determined data.
> The fact that you initially placed them into ideal geometry is not
> really
 any different from the non-H atoms of individual protein residues
> in your model, whose original positions were also based on known
> stereochemistry. 
> On the other hand, if you mean that the hydrogens you used for
> refinement
 were deleted and replaced during validation by Molprobity
> (which I think it may do by default) that's not good.  You should rather
> keep the hydrogen positions from refinement, not the ones from Molprobity.
> 
> Assuming (since this is ccp4bb) you refined with refmac...
> - If you are at the level of investigating hydrogen positions, you may
> want
 to consider taking the refinement into shelxl.
> - If you are not making claims about hydrogens but just want to
> describe
 what you did during refinement, I'd go with taking them out and
> settling for the standard record in the resulting PDB file:
>   REMARK   3  HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
> which looks like this in the corresponding mmcif file:
>   _refine.details   'Hydrogens have been added in their riding
> positions'
 
> Ethan
> 
> 
> >
> >
> > Thanks,
> > Matthew
> >
> >
> >
> > ---
> > Matthew J. Whitley, Ph.D.
> > Research Instructor
> > Department of Pharmacology & Chemical Biology
> > University of Pittsburgh School of Medicine
> >
> >
> >
> >
> > ##
> > ##



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Hydrogens in PDB File

[Ethan A Merritt]

On Thursday, 27 February 2020 15:35:05 PST Whitley, Matthew J wrote:
> Hello all,
> 
> I am nearly finished refining the structures of two mutant proteins from
> crystals that diffracted to very high resolution, 1 Å and 1.2 Å,
> respectively.  Refinement was conducted in the presence of explicit
> hydrogens on the models.  I am preparing to deposit these models into the
> PDB but am unsure about whether to retain or remove the hydrogens for
> deposition.  On one hand, these hydrogens were explicitly used during
> refinement, so that makes me want to keep them, but on the other hand, they
> were added at theoretical positions by MolProbity’s reduce tool for
> refinement and were not positioned on the basis of experimentally observed
> electron density, so that makes me want to delete them from the
> experimental model.  Which is the preferred option for this situation?

The order of operations you describe is unclear.

If you explicitly refined hydrogens then their final positions are indeed
based on experimentally determined data.
The fact that you initially placed them into ideal geometry is not really
any different from the non-H atoms of individual protein residues in your
model, whose original positions were also based on known stereochemistry.

On the other hand, if you mean that the hydrogens you used for refinement
were deleted and replaced during validation by Molprobity (which I think it
may do by default) that's not good.  You should rather keep the hydrogen
positions from refinement, not the ones from Molprobity.

Assuming (since this is ccp4bb) you refined with refmac...
- If you are at the level of investigating hydrogen positions, you may want
to consider taking the refinement into shelxl.  
- If you are not making claims about hydrogens but just want to describe
what you did during refinement, I'd go with taking them out and settling
for the standard record in the resulting PDB file:
  REMARK   3  HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
which looks like this in the corresponding mmcif file:
  _refine.details   'Hydrogens have been added in their riding positions'

Ethan

> 
> Thanks,
> Matthew
> 
> ---
> Matthew J. Whitley, Ph.D.
> Research Instructor
> Department of Pharmacology & Chemical Biology
> University of Pittsburgh School of Medicine
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

[Ethan A Merritt]

On Monday, 16 December 2019 09:25:59 PST Jessica Besaw wrote:
> Dear community,
> 
> I am having a lot of trouble solving a protein structure. I think my
> problem may caused by incorrectly placed proteins in molecular replacement.
> I have two proteins in my asymmetric unit. It appears that one protein fits
> perfectly, and the other one has many errors. (See snapshots below). I have
> tried deleting the parts of the protein (and even the whole protein) to try
> and rebuild it in COOT, but it was a bit too difficult for me to solve.
> 
> I would appreciate any and all suggestions for potential strategies moving
> forward.
> 
> Other information:
> (1) 2.4 Angstrom
> (2) 99% complete
> (3) "Translational NCS may be present at a level that may complicate
> refinement"

Try turning off the translational NCS check.
We have had two structures where incorrect diagnosis of tNCS prevented
Phaser from finding the correct solution.  If you are not using Phaser, the
caveat still stands in principle.

Ethan


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Xray-dataset usable despite low completeness ?

[Ethan A Merritt]

On Thursday, 28 November 2019 16:51:15 Jurgen Bosch wrote:
> 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 :-)

Don't forget that it helps to evaluate turkey quality
if you can taste matched samples from both sides. 
The cc1/2 "cooking comparison" test cannot be conducted
properly if one leg is missing.  The turkey is still
just as good but the yumminess is on a subjective scale.

(turkey sampling is still hours away here)

Ethan


> 
> Happy Thanksgiving everyone
> 
> Jürgen 
> 
> P.S. back to my wine & ducks to be roasted. @BR, mit Rotkraut & 
> Kartoffelknödel
> 
> > On Nov 28, 2019, at 4:38 PM, Bernhard Rupp  wrote:
> > 
> > Sorry for being late on this thread - 
> > 
> > but the completeness myth is one of these conventional wisdoms I am 
> > seriously questioning and completeness
> > as a global statistic is almost uninformative, short of telling you 'fewer 
> > than all recordable reflections up to the reported 
> > (likely isotropic) resolution limit given whatever (likely isotropic) 
> > cutoff was applied'. Sounds not very clear to me. 
> > 
> > Kay mentioned already that any information is better than no information, 
> > with the caveat that you cannot expect
> > map quality (being an upper limit for model quality - not going into 
> > precision vs accuracy issue here) corresponding to 
> > the highest resolution reported, which is in reality frequently anisotropic 
> > (but not reported or reflected adequately 
> > in the PDB reports). 
> > We posted some remarks to this effect recently, pointing out that highly 
> > incomplete and anisotropic data can still 
> > yield limited but useful information as long as your claim remains 
> > correspondingly modest. Section 3.4 in
> > http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html
> > 
> > Having said that, while random incompleteness is not problematic, 
> > systematic reciprocal space incompleteness leads
> > to corresponding systematic real space effects on the map, the simplest 
> > being anisotropic data reflecting anisotropic
> > reciprocal map resolution. This is different for example when wedges are 
> > missing or absence of serial extinctions makes
> > space group determination more challenging (although we are almost in the 
> > age where 'record 360 deg of data and 
> > try every SG' works). James Holton has video examples for incompleteness 
> > effects and some images are also in my book.
> > https://bl831.als.lbl.gov/~jamesh/movies/
> > 
> > Cheers & Happy Thanksgiving, BR
> > 
> > PS: A systemic rant regarding data quality representation can be found here
> > https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2
> > 
> > --
> > Bernhard Rupp
> > http://www.hofkristallamt.org/
> > b...@hofkristallamt.org
> > --
> > All models are wrong
> > but some are useful.
> > --
> > 
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Kay 
> > Diederichs
> > Sent: Monday, November 25, 2019 08:07
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
> > 
> > Dear Matthias,
> > 
> > Of course, high completeness is better than low completeness.
> > But as long as your low resolution is pretty much complete, there is no 
> > such thing as "too low completeness" at high resolution. Each reflection 
> > adds information to the map, and serves as a restraint in refinement.
> > 
> > best,
> > Kay 
> > 
> > 
> > On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke 
> >  wrote:
> > 
> >> Dear ccp4 Bulletin Board,
> >> 
> >> I collected a dataset at a synchrotron beamline and got the statistics
> >> (CORRECT.LP) after processing (using xds) shown in the attached 
> >> pdf-file.
> >> 
> >> Do you think this dataset is usable, due to its low completeness? As 
> >> you can see in the attached file the completeness is just 50% in the 
> >> highest resolution shell, whereas the I over Sigma is above 2 and also 
> >> the CC 1/2 (80%) and the R factors (36.8%) have reasonable values.
> >> Furthermore the overall statistic are good regarding R factor, CC 1/2 
> >> and I over Sigma. The only problem seems to be the completeness. If I 
> >> would set the cut-off at a lower resolution to get good completeness, I 
> >> would throw away nearly half of my reflections.
> >> 
> >> I'm happy to here your opinion. In Addition to that: The space group is 
> >> orthorhombic and the dataset was collected over 120° using fine slicing 
> >> (0.1°).
> >> 
> >> 
> >> Best regards,
> >> 
> >> Matthias Oebbeke
> >> 
> >> 
> > 
> > #

Re: [ccp4bb] Resonant Scattering Directionality

[Ethan A Merritt]

On Thursday, July 25, 2019 11:23:34 AM PDT Keller, Jacob wrote:
> Dear Crystallographers,
> 
> It seems to be a usual assumption that anomalous scattering is essentially 
> angularly-independent, e.g.:
> 
> http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm
> 
> But why the can't we see anomalous-only spots at e.g. 1 Ang resolution in a 2 
> Ang data set?

Because the resolution limit of visible data is detemined by the ordering
of the sample crystal, not by the angular dependence of the scattering factor.
A crystal that only produces spots to 4Å does so because it's a lousy crystal,
not because it somehow tricked the constituent atoms into having different
scattering factors.

Ethan


> 
> This actually has some repercussions for a non-x-ray (but still resonance) 
> idea, so it would be helpful to know...
> 
> All the best,
> 
> Jacob
> 
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> Desk: (571)209-4000 x3159
> Cell: (301)592-7004
> +
> 
> The content of this email is confidential and intended for the recipient 
> specified in message only. It is strictly forbidden to share any part of this 
> message with any third party, without a written consent of the sender. If you 
> received this message by mistake, please reply to this message and follow 
> with its deletion, so that we can ensure such a mistake does not occur in the 
> future.
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] COOT over SSH

[Ethan A Merritt]

On Friday, June 7, 2019 1:40:28 AM PDT Pedro Matias wrote:
> This is a known problem when accessing recent Linux releases remotely
> via ssh -X.
> 
> The default X-server configuration has changed and openGL applications
> no longer work. Supposedly it should be possible to revert the server
> behaviour with a flag on startup but I haven't been able to do so.
> 
> I found a nice piece of software called vglrun that works around this
> problem and restores the old behaviour of openGL applications like coot
> and PyMol, e.g. 'vglrun coot' or 'vglrun pymol'.

The problem there is that vglrun requires that you have a decent graphics
card on the server, which is used to generate the display image for
export to the client display machine.  My compute servers don't have any
graphics cards, so this doesn't work.  In the future I guess this problem
provides a reason to buy graphics even for a machine that is only a
"compute server", but that doesn't help with existing configurations.

anyhow good to hear that vglrun works with coot

Ethan

> 
> HTH,
> 
> Pedro
> 
> Às 21:52 de 06/06/2019, Paul Emsley escreveu:
> > On 06/06/2019 21:35, Chen Zhao wrote:
> >>
> >> I have not been able to open COOT through SSH, in cases where COOT is
> >> version 0.8.9.2-pre-revision-7884 packaged with SBGrid mounted on a
> >> server running scientific linux.
> >
> > possibly relevant:
> >
> > https://mail.ncmir.ucsd.edu/pipermail/3dem/2019-February/006519.html
> >
> > ############
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] translational NCS & twinning

[Ethan A Merritt]

On Thursday, January 10, 2019 2:11:52 AM PST Donghyuk Shin wrote:
> Dear all,
> 
> I am having tough time with my Xtal data sets those seem to be twinned or 
> have translational NCS, and it will be greatly appreciated if you can give me 
> some advices or comments!
> 
> Data was initially processed with XDS and scaled with aimless without 
> specifying certain space group (SG).
> Aimless picked the P 63 2 2 for the best SG, but the xtriage indicates there 
> is non-origin peak after patterson analysis. (attached log)
> And, I could not get the proper MR-solution from this data sets.
> 
> Because I read that twinning and tNCS cannot be properly distinguished at 
> high SG, I went down to subgroup either P32 or P6 assuming that there is 
> twinning which make data set seems to have apparently high SG. (procedure was 
> same XDS->aimless but I specified the SG to keep them)
> Then, xtriage still indicates there is non-origin peak as before, but found 
> twin laws for the data sets (attached log).
> However, I still could not get the right MR-solution.
> Then, I went even further down to P3 or C2, and xtriage found more twin laws 
> which is make sense because of the lower SG. (attached log)

> Again, I could not get the MR-solution.
> For all the MR running above, I assumed that phaser(ccp4 module) 
> automatically applied tNCS if they present. or should I have to tick on 
> button in the expert parameters?
   ^^^

Hi Donghuk,

This may indeed be a possible source of problems.   I have recent experience 
with a
case where aimless/xtriage/phaser all report a large tNCS component, but 
allowing
phaser to use this information prevents finding a correct MR solution.  I can 
only
obtain the known correct solution by telling phaser explicitly _not_ to use 
tNCS.
In my case the true space group is P1 but the angles are all close to 90., 
causing
most indexing programs to falsely identify it as P2.  I cannot say how or why 
the
tNCS test triggers, but the known correct solution in P1 does not contain tNCS.

Ethan


> 
> Then, I went back to the image and processed the datasets with mosflm by 
> checking the indexed spots.
> During this step, I played with the threshold for indexing to follow the 
> strong spot for get correct SG.
> I am not sure whether this is correct or not, but by putting high threshold 
> for indexing (e.g. ~15) I could index the data with C2 which has half 
> dimension for a,b axes (116.348,  67.218, 182.861,  90, 90, 90) to the 
> original unit cell (232.533, 134.202, 182.67, 90, 90, 90).
> With this, I could put 3 molecules in ASU by MR. During refinement, I felt 
> that the R values were not dropping, and I applied twin refinement.
> without twin refinement the R values were (0.39/0.44, work/free), and 
> applying twin refinement gave me significantly better values (0.23/0.26).
> Because there were 6 twin operators which may cause this huge R value drop, I 
> speculate whether this is true or not.
> 
> Your comments will be greatly helpful! 
> 
> With you all the best,
> Donghyuk
> 
> 
> 
> ########
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Off topic question

[Ethan A Merritt]

On Thursday, January 3, 2019 12:40:05 PM PST Reza Khayat wrote:
> ?Hi,
> 
> 
> Happy new year to all!  A bit of an off topic question.  Does anyone know of 
> a method/program to extract the most distinct "n" (n>2) sequences from a 
> sequence alignment?  Thanks.

If these putative "most distinct" sequences are hypothesized to belong
together,  then i suggest K-means clustering.  If they are hypothesized
to be unrelated individual outliers then I think you would just take the
worst scores using whatever metric you used to create original alignment.

Ethan

> 
> 
> Best wishes,
> Reza
> 
> 
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] VERY old mtz file..

[Ethan A Merritt]

On Tuesday, November 13, 2018 1:06:01 PM PST Zhijie Li wrote:
> Hi Ethan,
> Thanks for the information. My guess is that in MTZ only F-float is expected, 
> because it is the only 32bit form? 

I do not remember exactly what was used for mtz files at that time.
It might have been REAL*4 or it might have been REAL*8.
<\me rummages along the shelf above my desk>
Looking here at my trusty VAX-11 Fortran manual from April 1982,
D_floating was the default for REAL*8.

F_floating: 1 bit sign,  8 bit exponent,  23 bit mantissa
D_floating: 1 bit sign,  8 bit exponent,  55 bit mantissa 
G_floating: 1 bit sign, 11 bit exponent, 52 bit mantissa

Later on they introduced H_floating, S_floating, T_floating and probably an 
entire
zoo that went extinct shortly after.

Bit assignments:
https://nssdc.gsfc.nasa.gov/nssdc/formats/VAXFloatingPoint.htm


Ethan


> Zhijie
> 
> > On Nov 13, 2018, at 3:44 PM, Ethan A Merritt  
> > wrote:
> > 
> >> On Tuesday, November 13, 2018 11:51:55 AM PST Zhijie Li wrote:
> >> If somebody is going to send these files by email, please send one to me 
> >> too. Thanks in advance. I actually prefer to get a MTZ file because the 
> >> miller indices would serve as good clues for understanding the encodings.  
> >> Even the first 1024 bytes of an MTZ would do (data array starts at byte 80 
> >> in MTZ).
> >> 
> >> In my life I had only seen ieee754.  According to what I can find, VAX has 
> >> an exponent bias of 128 (ieee754 uses 127). Then it seems to me that when 
> >> converting from vax to ieee a division of 2 is involved.
> > 
> > It's more complicated than that.  VAXen supported multiple floating point 
> > formats,
> > F-floating G-floating and H-floating.
> > They had differed by how many bits were used for the exponent, and hence how
> > many bits were left for the mantissa.
> > I can pull out the architecture manuals if necessary.
> > 
> >ah, nostalgia
> > 
> >Ethan
> > 
> > 
> >> However all procedures I have seen use a division of 4, which is quite 
> >> puzzling to me. A real data file containing meaningful numbers (eg., HKL 
> >> indices) would be very helpful. Thanks in advance.
> >> 
> >> Zhijie
> >> 
> >>> On Nov 13, 2018, at 2:21 PM, Johan Hattne  wrote:
> >>> 
> >>> Related by not exactly on topic: would anybody on the list be able to 
> >>> share old map files (not MTZ:s) with Convex, Cray, Fujitsu, or VAX 
> >>> reals/strings?  I’d be interested to see what those files actually 
> >>> look(ed) like.
> >>> 
> >>> // Best wishes; Johan
> >>> 
> >>>> On Nov 9, 2018, at 18:38, Zhijie Li  wrote:
> >>>> 
> >>>> Hi all,
> >>>> 
> >>>> On linux there are a few good GUI HEX editors. Here I’d like to 
> >>>> recommend BLESS, which conveniently displays all possible numerical 
> >>>> interpretations of the four bytes under cursor. It also allows the user 
> >>>> to switch between big endian or little endian through a checkbox. 
> >>>> Unfortunately all floats are assumed to be IEEE754, therefore VAX floats 
> >>>> won’t be interpreted correctly.  ( The simplest way to convert vax to 
> >>>> ieee float would be to write a little program to do some bit operations. 
> >>>> I’d be happy to take that as my weekend project)
> >>>> 
> >>>> 
> >>>> BTW, along the line of space efficiency, I can’t help noticing that the 
> >>>> miller indices are saved as float32 in mtz, as all other numbers in mtz. 
> >>>> This certainly have made mtz format a beautiful homogeneous data format 
> >>>> ;).  In this particular case, if we have doubts about the reliability of 
> >>>> the machine stamp, trying to restore the miller indices would be a good 
> >>>> way to test hypotheses.
> >>>> 
> >>>> Zhijie
> >>>> 
> >>>>> On Nov 9, 2018, at 9:04 PM, James Holton 
> >>>>> <270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>>>> 
> >>>>> As a beamline scientist I must say I am glad that diffraction image 
> >>>>> data is not usually stored as ASCII text.  In fact, I am slowly warming 
> >>>>> to the idea of storing it as not just binary, but compressed formats.  
> >>>>> Problem, I'm sure will be that it won't be  long before we forget how

Re: [ccp4bb] VERY old mtz file..

[Ethan A Merritt]

gt;> swapping
> >>> I'm sure there are other combinations, but the oldest MTZ I have is only 
> >>> from 1996.
> >>> 
> >>> -James Holton
> >>> MAD Scientist
> >>> 
> >>> 
> >>>> On 11/9/2018 4:47 AM, Eleanor Dodson wrote:
> >>>> Anyone any idea what to do about this?? Created in 1992!!
> >>>> Seems unreadable..
> >>>> 
> >>>> No CTYP lines input for file:  1
> >>>>Indices output even if all data items flagged "missing"
> >>>> Warning, NOT all LABOUT data lines given
> >>>> Warning: Machine stamp corrupted? Assuming native format. 
> >>>>>>>>>> CCP4 library signal library_file:End of File (Error)
> >>>> 
> >>>> 
> >>>> To unsubscribe from the CCP4BB list, click the following link:
> >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >>>> 
> >>> 
> >>> 
> >>> To unsubscribe from the CCP4BB list, click the following link:
> >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >>> 
> >> 
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >> 
> > 
> >  Research Specialist @ Gonen Lab
> > 
> >  UCLA * 615 Charles E. Young Drive South
> > BSRB #347 * Los Angeles, CA 90095
> > 
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] VERY old mtz file..

[Ethan A Merritt]

On Friday, November 9, 2018 9:12:36 AM PST Robert Esnouf wrote:
> 
> Without checking further, there is a "dd" option for swapping big-endian to 
> little-endian... swab. This may simply be the issue... 

DEC computers used a different floating point format.
Swapping endian-ness would be sufficient, although it might be required in 
addition.

Ethan


> 
> The output of od -x may help decode the header of the file...
> 
> Regards,
> Robert
> 
> --
> 
> Dr Robert Esnouf 
> 
> University Research Lecturer, 
> Director of Research Computing BDI, 
> Head of Research Computing Core WHG, 
> NDM Research Computing Strategy Officer 
> 
> Main office: 
> Room 10/028, Wellcome Centre for Human Genetics, 
> Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK 
> 
> Emails: 
> rob...@strubi.ox.ac.uk / rob...@well.ox.ac.uk / robert.esn...@bdi.ox.ac.uk 
> 
> Tel:   (+44)-1865-287783 (WHG); (+44)-1865-743689 (BDI)
>  
> 
> -Original Message-
> From: "Pavel Afonine" 
> To: CCP4BB@JISCMAIL.AC.UK
> Date: 09/11/18 13:54
> Subject: Re: [ccp4bb] VERY old mtz file..
> 
> Now I see the value of storing data in plain text files even more (mind Shelx 
> or X-plor formats, for example) -;)
> 
> 
>  readable files.>
> 
> On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein  
> wrote:
> 
> Hi Eleanor,
> 
> You could try running the oldest MTZ2VARIOUS binary you can find -
> e.g.
> 
>   wget ftp://ftp.ccp4.ac.uk/ccp4/4.2/binaries/ccp4-4.2_Linux.tar.gz
>   tar -xvf ccp4-4.2_Linux.tar.gz bin/mtz2various
> 
>   bin/mtz2various hklin ...
> 
> Any older binaries (ftp://ftp.ccp4.ac.uk/ccp4/4.0.1/) will require an
> SGI or Dec/Alpha machine ;-)
> 
> If that doesn't help I would first check that it is actually a correct
> MTZ file: does the ASCII header (trailer) show up with
> 
>   strings your.mtz
> 
> towards the end?
> 
> Cheers
> 
> Clemens
> 
> On Fri, Nov 09, 2018 at 12:47:09PM +, Eleanor Dodson wrote:
> > Anyone any idea what to do about this?? Created in 1992!!
> > Seems unreadable..
> >
> > No CTYP lines input for file:  1
> > Indices output even if all data items flagged "missing"
> >  Warning, NOT all LABOUT data lines given
> > Warning: Machine stamp corrupted? Assuming native format.
> > >>>>>> CCP4 library signal library_file:End of File (Error)
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
> --
> 
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] A question related to Fe-S proteins

[Ethan A Merritt]

On Monday, March 19, 2018 2:20:50 PM PDT PULSARSTRIAN wrote:
> Dear Professor Diana,
> 
> Thank you very much for your
> comment, and we will certainly look at, if ‘domain swapping’ is any reason
> for the trimeric nature of the protein.
> 
>   There are two cysteines in helix-1 and two cysteines
> in helix 3. From our mutational studies (C to S), we confirmed in the *in
> vivo *assembled protein, that only helix-1 (the first two cysteines) form
> the Fe-S cluster. So, its altogether a completely new structure compared to
> reconstituted protein.

Your description of the in vivo characterization seems to be inconsistent.

1) 4Fe-4S cluster formed in vivo from 2 copies of helix-1, each contributing 2 
Cys. 
2) resulting in a trimer

How would that work?

Or is it that you are proposing that there is a single 4Fe/4S center per trimer,
formed stochastically from 4 of the 6 available Cys residues?

You don't mention having EPR for the in vivo assembly.
Have you determined the Fe/S stoichiometry in the trimer?

Ethan

> 
> Regards,
> 
> Bhanu
> 
> 
> 
> On Mon, Mar 19, 2018 at 10:13 PM, Diana Tomchick <
> diana.tomch...@utsouthwestern.edu> wrote:
> 
> > Is it possible that you have a case of domain swapping that causes the
> > trimeric assembly?
> >
> > Diana
> >
> > **
> > Diana R. Tomchick
> > Professor
> > Departments of Biophysics and Biochemistry
> > University of Texas Southwestern Medical Center
> > 5323 Harry Hines Blvd
> > <https://maps.google.com/?q=5323+Harry+Hines+Blvd&entry=gmail&source=g>.
> > Rm. ND10.214A
> > Dallas, TX 75390-8816
> > diana.tomch...@utsouthwestern.edu
> > (214) 645-6383 (phone)
> > (214) 645-6353 (fax)
> >
> > On Mar 19, 2018, at 3:07 PM, PULSARSTRIAN 
> > wrote:
> >
> > Dear all,
> >
> > Sorry for the slightly off-topic question.
> >
> >I am working on a non-native, *de novo* [4Fe-4S]
> > protein, designed as a four-helix bundle. The * in vitro* reconstituted
> > protein assembles with [4Fe-4S] (confirmed by EPR) and exists in
> > monomer-dimer configuration (confirmed by SEC). These results have been
> > already published.
> >
> >Recently we could get the [4Fe-4S] assembly directly from
> > the *E. coli* (*in vivo* assembly). Everything is as expected (compared
> > to reconstituted protein), except the oligomerization state. The protein
> > assembles as trimer, in contrast to monomer-dimer configuration of the
> > reconstituted protein. The trimeric nature of the *in vivo* assembled
> > protein has been confirmed by SEC, SEC-SLS and SAXS.
> >
> >
> >  *So, my question is, has anyone encountered such situation,
> > where the As-purified Fe-S protein having a completely different oligomeric
> > state compared to the in vitro reconstitution protein? *
> >
> >
> > Looking forward to hearing for some examples and/or references.
> >
> >
> > Regards,
> >
> > Bhanu
> >
> >
> > --
> >
> > UT Southwestern
> >
> > Medical Center
> >
> > The future of medicine, today.
> >
> 
> 
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] 3D Structure Search

[Ethan A Merritt]

On Thursday, February 15, 2018 3:16:50 PM PST Nicola Evans wrote:
> I have recently solved a novel structure which previously did not have any 
> structural homologues (as related by sequence identity). I was wondering if 
> anyone could recommend a 3D structural search engine? I used the Dali server 
> which has been recommended to me in the past (and with past success) but the 
> top few hits this time aren't similar structurally (although I haven't 
> exhausted the list yet). I just want to confirm if the folds are truly novel 
> or not.

Dali is sensitive to the order of secondary structure elements.
This is relevant if you are looking for evolutionary relatedness, but 
not if you just want to ask "does it look like this". 

For the latter question, I suggest the VAST server at NCBI.
https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] microdiffraction data assembly method

[Ethan A Merritt]

On Tuesday, November 21, 2017 9:32:15 AM PST CPMAS Chen wrote:
> Hi, CCP4ers,
> 
> I came across this paper about improving data by microdiffraction data
> assembly method from Raymond C. Stevens group,
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338336/#SD1.
> 
> By reading their methods, this seems to me like manually selecting data
> based on Rmerge. After almost 5 years, do we have a better/quicker
> script-based method to do so?

The difficulty they faced was essentially identical to that faced by all
the nanocrystal + XFEL experiments performed since then.
The data processing software being developed for XFEL probably does
what you are asking for.  You might start here:

  http://viper.lbl.gov/cctbx.xfel/index.php/Main_Page

The issue is that each crystal contributes only a small slice of 
reciprocal space to the data.   In the case of XFEL data this is only
a still image.  In the paper you cite it was more than that, but still
very small compared to "normal" data sets.

Ethan 
 
> Their data improved not only in resolution, but also in the statistics. The
> method seems impressive.
> Thanks!
> 
> Charles
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] normalization of B-factor values from different crystal structures

[Ethan A Merritt]

On Wednesday, 02 August, 2017 21:58:07 Asmita Gupta wrote:
> Hi,
> 
> Thanks for the response! 
> 
> What I have are crystal structures of the same protein in multiple 
> conformations, solved by different groups. I wanted to calculate the 
> residue-wise B-factors for each of these structures and compare how the 
> values are changing for corresponding residues in these different structures. 
> e.g. B-factor variation in residue number 200 (Ala) in 10 different 
> conformations of a protein. 
> 
> Hope I have been able to answer the question!

But what is the biological question?  
You haven't learned much if all you can say is
"The B factor of residue 200 is higher in this structure".

Do you not have a larger question in mind - on the order
of "ligand binding a site X correlates with reduced 
mobility of loop A-B"?   

For such questions I suggest (as I always do :-) using TLSMD
analysis rather than examining individual B factors.  
That allows you to say something like "in structure #1 we
can identify a distinct group motion of residues in loop A-B,
whereas in structure #2 loop A-B appears to move in concert
with the entire subdomain XX".  This is not the same thing
as saying individual B factors are higher or lower.

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] refmac output

[Ethan A Merritt]

On Wednesday, 02 August, 2017 16:12:30 Edwin Pozharski wrote:
> Just to clarify, how do you use the extra columns in this scenario?  My
> suggestion was to have the output file that includes only the map
> coefficient columns, so you still can look at the map.  IIRC, FP/SIGFP
> columns from refmac output are actually modified from the input (scaled
> with Boverall), so it was not recommended to use refmac output as input of
> any kind.

The scaled Fs are useful to recalculate R as a function of whatever, and
to calculate alternative R values (e.g. for Hamilton R test or comparison
to shelxl R1 R2). It's nice to carry though DANO and SIGDANO so that one
can generate anomalous maps. In general I'd rather err on the side of
including everything rather than discarding something that may be useful
later.  In any case it's trivial to run one additional script to filter
unwanted columns if file size really is a controlling factor.

Ethan




> 
> Also, to provide context, my comment resulted from dealing with a large
> chunk of data that included ~200 output mtz files - which is Gb-sized
> tarball that had to be uploaded/downloaded.  Not the end of the world, but
> cutting it in half seemed like a good idea at the time. :)  Not hard to
> script that, of course.
> 
> I am not necessarily advocating for skinny files to be the default, but as
> it stands, refmac/buster/phenix do not even provide the option of doing it
> (It's entirely possible that I am wrong here on specifics and will get
> corrected by Garib, Gerard and Pavel).
> 
> Cheers,
> 
> Ed.
> 
> Edwin Pozharski, PhD, Assistant Professor
> University of Maryland, Baltimore
> --
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
> When harmonious relationships dissolve then respect and devotion arise;
> When a nation falls to chaos then loyalty and patriotism are born.
> -- / Lao Tse /

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] normalization of B-factor values from different crystal structures

[Ethan A Merritt]

On Wednesday, 02 August, 2017 12:09:35 Asmita wrote:
> Hi,
> 
> This might look as a very fundamental question. I have a dataset of crystal
> structures better than 3.5Ang resolution. For a qualitative analysis, I
> want to compare the residue-wise B-factors in these structures, but due to
> different procedures adopted in refinement and scaling, I understand that
> these values cannot be compared in a raw manner.
> 
> Can someone suggest appropriate normalization methods that could be used
> for scaling these B-factors for a relevant and meaningful comparison? All
> the files have isotropic B-factor values and there are no ANISOU entries in
> any of the files.

I may have an answer, but I first I need a better handle on the question.

Can you take a step back and explain what question or hypothesis you
would like to address by making the comparison?  

Do you want to compare B factors for different residues in the same structure,
or B factors for the same residue in different structures,
or something else entirely?

    Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] CYS modification and choice of PEG

[Ethan A Merritt]

On Wednesday, 17 May, 2017 20:03:42 Antonio Ariza wrote:
> I haven't asked anything for a loong time, so here are a couple of 
> question "for the honourable members of the esteemed CCP4 bulletin board" ... 
> or as I'd usually say: "for y'all".  ;)
> 
> 1)  I have this modified CYS in one of the structures I'm working on and ... 
> I'm quite unhappy with it (see attached pics). At first I thought it was 
> cacodylate ... but alas, no cacodylate was used during purification or 
> crystallisation. So I looked up possible modifications on CYS residues and I 
> came up with cysteine-s-sulfonic acid (CSU). This looks good in principle but 
> it doesn't quite fit the electron density as the bond between the two sulphur 
> atoms is too short. The average length for an S-S bond is about 2.05 Ang and 
> refmac refines this one to 1.97 Ang, but it looks like it should be at least 
> 2.5 Ang to sit correctly in the electron density. Also, there is some 
> negative density in there, suggesting that maybe it's something with fewer 
> electrons than a sulfonic acid ... or maybe it has less than 100% occupancy. 
> Any suggestions?

Could it be that a cloning error introduced a Cys->Arg mutation?

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Coot render tool missing

[Ethan A Merritt]

On Monday, 27 March, 2017 22:12:22 Paul Emsley wrote:
> On 27/03/17 21:55, Xiao Lei wrote:
> >
> >
> > Because the picture quality from Coot>>Draw>>Screenshot>>Simple is 
> > very low, I tried Coot>>Draw>>Screenshot>>Povray or Raster3D to export 
> > high quality picture, but I had an error of "render tool missing" and 
> > Coot tried automatically find the render tool but failed. I use 
> > Wincoot 0.8 version in Win7. I do know if any of you have similar 
> > experience.
> >
> >
> 
> The render program is part of Ethan Merritt's Raster3D package/suite.  
> The build system in coot that attempts to compile it is a bit fragile.
> 
> http://skuld.bmsc.washington.edu/raster3d/

That is the source package, yes.

The Raster3D programs are now in the CCP4 bundle also.
If render is not being found, you may have a PATH error.
Is your Coot finding other CCP4 programs?

Ethan


> 
> Paul.
> 
> p.s. Draw -> Additional Representation -> Ball & Stick makes things a 
> bit nicer, as does Extensions -> Representation -> Highlight Interesting 
> Site (still not as nice as a proper molecular graphics program though).

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] B-factors/Occupancies Versus "Local Resolution"

[Ethan A Merritt]

On Monday, 06 March, 2017 19:54:23 Keller, Jacob wrote:
> Dear Crystallographers (and cryo-EM practitioners,)
> 
> I do not understand why there is a discrepancy between what crystallographers 
> use to models disordered regions (b-factors/occupancies) and what the cryo-EM 
> world uses ("local resolution.") 

In both the EM and the X_ray world "uncertainty" is a property of the model,
while "resolution" is a property of the data.

For a crystal structure the resolution is known as soon as you collect the data;
you don't even need to solve the structure.  It is a single number, or if you
want to get fancy an anisotropic tensor.  In neither case is it a model for
disorder.

As I understand it (I am definitely out of my comfort zone here) EM does not
have easily determined uniform resolution.  Instead you estimate the resolution
by looking at the image-to-image correlation after superposition, where the
correlation is computed only over some local region.  You can have a core 
region where images superimpose well and thus have high correlation (good
resolution), and at the same time have distal regions where there is 
image-to-image
variation yielding imperfect superposition, lower correlation, and poor
resolution.  That local resolution can still be calculated in advance of
fitting a molecular model. When you do fit a molecular model you may
deal with uncertainty by including B factors (well, ADPs) and occupancies
just as you would for a crystal structure.

Ethan


> I am tempted to say that "local resolution" is a misnomer, since I have been 
> trained to think of resolution as a simple optical or physical characteristic 
> of the experiment, and things that are blurry can in fact be "resolved" while 
> disordered-one might think of the blurred wings of an insect in a 
> long-exposure photograph, in which the resolution is of course ample to see 
> the wings-but is there a good reason why the two different terms/concepts are 
> used in the different fields? Could crystallographers learn from or 
> appropriate the concept of local resolution to good benefit, or perhaps vice 
> versa? Anyway, if there is a good reason for the discrepancy, fine, but 
> otherwise, having these different measures prevents straightforward 
> comparisons which would otherwise be helpful.
> 
> All the best,
> 
> Jacob Keller
> 
> 
> 
> 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Estimating the amount of missing electron density for a model

[Ethan A Merritt]

Thank you Randy and Pavel for correcting my failure to find an
appropriate tool in my mental toolbox.  I was thinking too much
in terms of examining a difference map rather than a performing
a resolution-dependent analysis of Fo;Fc agreement.

Is there a straight-forward way to extract what Hunter wants from
the output of SIGMAA run from the ccp4i interface?

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Estimating the amount of missing electron density for a model

[Ethan A Merritt]

On Tuesday, 21 February, 2017 16:53:06 Hunter Moseley wrote:
> Is there a straight-forward way to estimate the amount of missing electron
> density that a particular protein structure is missing based on the
> difference between Fo and Fc?

Short answer: no.
 
> It appears that the normalization of the Fc due to the employing of a
> maximum entropy method that keeps Fo and Fc comparable to the standard
> deviation of Fo would make this difficult.

Maximum entropy is not the issue.  Your Fobs have no intrinsic scale.
They are not a count of photons-per-second or a fractional intensity of
the direct beam.  In order to refine a model you must introduce an
ad hoc scale factor to make Fobs approximately equal to Fcalc on average. 
"On average" is a somewhat sloppy description (that's where use of
maximum likelihood weighting may come in) but in the end we normally
calculate and display difference-density maps such that the mean
difference density is zero.  You won't end up with a map that is
overall negative even if your model has spurious extra bits and you
won't end up with a map that is overall positive even if your model
is missing large chunks.  The best you can hope for is that your
missing chunks will manifest in the map as connected blobs of positive
difference density balanced out by diffuse/disconnected regions of
negative difference density elsewhere.

Longer answer: still no.  

The distribution of differences between Fobs and Fcalc can provide an
estimate of how good/bad wrong/right your current model is.
But that still doesn't tell you whether the current model is bad because
pieces are missing or bad because existing pieces are in the wrong place.


Ethan


> Or am I missing something?
> 
> Cheers,
> Hunter
> 
> 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

[ccp4bb] TLSMD server down with disk problems

[Ethan A Merritt]

The TLSMD server is suffering from hardware problems.
It is unclear how long it will take to fix this, or whether
the whole machine will need to be replaced.

I'd love it if someone would undertake to run a mirror
or equivalent server, but as it stands I think you're out of luck
until I can round up enough resources to fix/repair/replace mine.

sorry,

Ethan


On Thursday, 26 January, 2017 21:36:51 Carlos CONTRERAS-MARTEL wrote:
> Hi CCP4BB,
> 
> 
> Somebody know what happen with the TLSDM server at 
> http://skuld.bmsc.washington.edu/~tlsmd/
> 
> It has been refusing connections for already two days?
> 
> Perhaps a mirror exists somewhere ?
> 
> 
> Best
> 
> 
> Carlos
> 
> 
> 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Anisotropy and temperature

[Ethan A Merritt]

On Thursday, 19 January, 2017 20:35:14 you wrote:
> A PhD student asked me what causes diffraction anisotropy.  Quoting from the 
> Diffraction Anisotropy Server webpage that it is caused by whole-body 
> anisotropic vibration of unit cells. He asked whether a colder cyrostream 
> could improve anisotropy. My answer would be yes, as colder temperatures 
> would lower the vibrations.
> 
> My two questions are; (1) am I right? and (2) if so, has it ever been done 
> before in practice?

I do not know if there is past work and literature that answers your
question with specific regard to whole-body anisotropic vibration of
unit cells.

However with regard to anisotropy in general you must consider two
components. 

(1) Vibration that is still present in the crystal, so that
atoms or larger groups are moving while the diffraction is measured.
The vibrational amplitude will be temperature dependent, but
the anisotropy may remain the same since it depends on the ratio of
vibration amplitude in different directions rather than the 
magnitude in any one direction. 

(2) Vibrational displacement of a group in one unit cell relative
to copies of the same group in other unit cells that was "locked in"
when the crystal was frozen.  The frozen crystal captures a 
sampling of states that were present at room temperature.
The diffraction experiment sees a positional average over space
that is equivalent to a single-copy average over time.
This component is not temperature dependent so long as the 
crystal stays frozen.

Diffraction measurements at a single temperature do not distinguish
between these two components.  In principle a series of diffraction
measurements from the same crystal at different temperatures would
allow partitioning the observed vibrational into the two components.
[Burgi (2000) Rev. Phys. Chem. 51:275]  So far as I know this has
been confirmed for small molecule crystals but is too difficult
experimentally to be worth the trouble for protein crystals
(and I've tried :-)

This equivalence of states sampled from a single copy over time
to multiple copies in a frozen crystal is the basis for TLSMD
analysis.  In the special case of a single molecule per unit cell
I suppose a one-group TLS treatment reduces to what you originally
asked about - vibration of whole unit cells - but in general
it does not.

    cheers,

Ethan


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon Process; was RE: [ccp4bb] Twinning Question

[Ethan A Merritt]

t; 
> misleads the viewer to an incorrect conclusion. The caption on YouTube 
> doesn't help.
> 
> It's not that the phase is locked at 0 below and 180 above the resonance 
> point;
> 
> it's just that far from resonance point the input and output phases are 
> decoupled.
> 
> The camera happened to catch times at which the driver and the suspended 
> object
> 
> were "in phase" or "out of phase" and the narrator pointed that out, but 
> neither
> 
> state is a general phenomenon. I think. But maybe I'm confused.
> 
> 
> 
> Ethan
> 
> 
> 
> 
> 
> > Of course this is trying to give some physical description for the 
> > electromagnetic field when I was complaining about a similar thing for 
> > quantum mechanics. A nice article by Freeman Dyson illustrates the 
> > difficulty of doing this for both approaches.
> 
> > http://www.damtp.cam.ac.uk/user/tong/em/dyson.pdf
> 
> >
> 
> > Colin
> 
> > -Original Message-
> 
> > From: Ethan A Merritt [mailto:merr...@u.washington.edu]
> 
> > Sent: 04 November 2015 21:59
> 
> > To: Nave, Colin (DLSLtd,RAL,LSCI)
> 
> > Cc: ccp4bb
> 
> > Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a 
> > Single-Photon Process; was RE: [ccp4bb] Twinning Question
> 
> >
> 
> > On Wednesday, 04 November, 2015 09:48:13 Colin Nave wrote:
> 
> > > Domenico
> 
> > > Thanks for the kind words!
> 
> > >
> 
> > > I still don't like descriptions such as " Therefore, the anomalous 
> > > scattered photon will still be able to resonate with another anomalous 
> > > scatterer within the crystal" This is an attempt to describe what happens 
> > > to a photon before it has been observed and is therefore an attempt to 
> > > interpret Quantum Mechanics. As Feynman said about his formulation - it 
> > > is ""merely a mathematical description, not an attempt to describe a real 
> > > process that we can measure. Niels Bohr "brainwashed an entire generation 
> > > of physicist into believing that the whole job was done 50 years ago" as 
> > > Murray Gell-Mann said. This might be a bit unfair but most physicists 
> > > accepted the Copenhagen interpretation and concentrated on carrying out 
> > > the necessary calculations from which we have all benefitted. Quantum 
> > > Mechanics works but treat the physical descriptions of the processes with 
> > > scepticism.
> 
> >
> 
> > > Regarding anomalous scattering I like the classical analogy in terms
> 
> > > of a damped driven oscillator. There is a good video of this sort of 
> > > thing at https://www.youtube.com/watch?v=aZNnwQ8HJHU , for a non damped 
> > > case showing the phase changes near resonance.
> 
> >
> 
> > I like the video, but it leaves me scratching my head a bit.
> 
> > One comes away from it expecting that there will be a 180° change in the 
> > phase of every Bragg reflection just from choosing a "long" or "short" 
> > wavelength x-ray source. [Or to be more precise a 180° change in the 
> > contribution of the anomalous scattering atoms to every Bragg reflection].
> 
> >
> 
> > I realize that if the phase were to flip for all atoms then by Babinet's 
> > principle the same underlying structure should be recoverable with either 
> > choice of phases, but does this really happen? Anyhow, that would not apply 
> > when only a subset of atoms in the structure have an absorption edge that 
> > is spanned to the two wavelengths in question. So does this demo really 
> > match up to what happens in an X-ray experiment?
> 
> >
> 
> > Ethan
> 
> >
> 
> > > A bit of damping is probably apparent but if anyone knows of a better 
> > > example for a damped oscillator I would be interested.
> 
> > >
> 
> > > Colin
> 
> > >
> 
> > >
> 
> > > -Original Message-
> 
> > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> 
> > > Dom Bellini
> 
> > > Sent: 03 November 2015 18:05
> 
> > > To: ccp4bb
> 
> > > Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a
> 
> > > Single-Photon Process; was RE: [ccp4bb] Twinning Question
> 
> > >
> 
> > > Dear All,
> 
> > >
> 
> > >
> 
> > >
> 
> > > Sorry for bringing back this old topic but I think I might have an 
&g

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon Process; was RE: [ccp4bb] Twinning Question

[Ethan A Merritt]

tes for the next photon to 
> >arrive.
> I was re-thinking through this, and I think one of these numbers is wrong, 
> viz, "A photon zips through a 1mm crystal in about 3fs." The speed of light 
> is 3x10^8 m/s, so this leads to ~3.3 ps for a 1 mm path, and not 3 fs, a 
> difference of ~10^6. Maybe it was just a typo? Anyway, it may not make a huge 
> difference, since this would still make for an average of ~1 photon in the 
> crystal at a time, assuming a high flux of 10^12 photons per second. But of 
> course there would be some Poisson statistics involved, and there would be 
> several photons a significant part of the time.
> Also, I wonder about relativistic effects: in the famous train-in-tunnel 
> thought experiment, a large train can fit in a short tunnel if it's going 
> close to the speed of light. Is this applicable here, such that many photons 
> are in some sense in the crystal at once? Or maybe this is a red herring.
> But, to change topics a bit: part of the reason I am wondering about this is 
> anomalous scattering. Since the resonance energy of an atom is a fixed 
> amount, how can one photon provide that energy simultaneously to the 
> requisite number (at least thousands, I would think) of resonant scatterers? 
> Something's very funny here.
> Or, come to think of it, perhaps resonant scattering is no worse than normal 
> scattering: if the energy is divided up between the all the 
> normally-scattering electrons, you even have a problem with the one-photon 
> picture, since the emerging radiation is still of the same energy. You want 
> to have everything being scattered with a certain energy, but you also want 
> all the scatterers to scatter. The concept of "energy" seems to get strange. 
> Does one then need two terms, in which "energy" is just a characteristic of 
> radiation, like a color, and then there is some other attribute like 
> "probabilistic intensity," which describes how much "photon" is there?
> It is striking to me how much depth these everyday occurrences really have 
> when one starts wondering about them.
> Jacob
> 
> 
> 
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities

[Ethan A Merritt]

On Tuesday, 07 July, 2015 13:05:55 Phil Jeffrey wrote:
> I'm updating some code to have limited mmCIF/PDB format interoperability 
> and have hit a snag.  While I can infer the connection between some data 
> items in the PDB header REMARK and the items in mmCIF I can't 
> definitively deduce some others.  In particular the mapping of
> REMARK  2  RESOLUTION
> seems a little ambiguous and the dictionary documentation doesn't help 
> in this regard.

So far as I know, anything that begins with "REMARK" is not guaranteed
to follow any standardized convention.  Different programs fill in 
different things here, and depositors can add new stuff.
The current PDB documentation states:

  REMARK 2 states the highest resolution, in Angstroms, that was used in 
  building the model. As with all the remarks, the first REMARK 2 record 
  is empty and is used as a spacer.

"Used in building the model" is nicely ambiguous, so I doubt that 
you can map it uniquely to any single value reported by some particular
program.

Ethan



> 
> Does anyone know where to find an explicit mapping of one data field to 
> another between the two formats ?  (I don't expect there to be a data 
> field in the PDB header for everything in mmCIF but I do for the reverse 
> case).
> 
> 
> Thanks
> Phil Jeffrey
> Princeton
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] twinned data refinement

[Ethan A Merritt]

On Wednesday, 10 June, 2015 17:35:25 Mengbin Chen wrote:
> Hello everyone,
> 
> I am refining a 2.5 angstrom structure whose phase is solved by molecular
> replacement with a search probe determined by SAD with 3 angstrom
> resolution. While I am able to see densities of a bunch of water molecules
> and ligands in the MR solved structure, which means that the phase is
> correct, the Rfree gets stuck at ~27%. 

Why do you think this is a problem?
It is true that turning on twin refinement is expected to yield lower
R factors, and thus 27% in the presence of twin refinement is worse than
27% without twin refinement.  But having said that, Rfree = 0.27 is still 
not so horrible.

If the starting point for your MR solution was a 3A model,
there may have been errors in sidechain placement or even 
backbone conformation that can be corrected now that you
have higher resolution data.  Don't assume that the starting
model was perfect.

You say that you can see density for a bunch of waters and ligands.
Are these in your refinemed model yet?

What does Molprobity (or coot or phenix) say about the quality of
your sidechain rotamers?

Have you tried adding a TLS description?

Ethan


> The crystal belongs to P3221 and has
> a twinning fraction of 19%, according to Xtriage. Currently I've been
> sticking to Phenix for refinement, and twin law (-h, -k, l) has been
> applied.
> 
> I was wondering if the CCP4 community would have any suggestions of how to
> refine this twinned structure, such as softwares to use, tricky strategies
> to choose, etc. I really appreciate any recommendations you would come up
> with my situation!
> 
> Thank you in advance!
> 
> Best,
> Mengbin
> 
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] XDS Rmeas in space group determination

[Ethan A Merritt]

On Wednesday, 13 May, 2015 18:17:04 Chen Zhao wrote:
> Hi Ethan,

Sorry, I'm coming in late on this so I might have missed an
earlier explanation of exactly what programs are involved.


> Yes. My question was simply whether it calculates the statistics 
  
> from completely unmerged intensities and just compare say h,k,l with -h,-k,l 
> (or -h,-k,-l and h,k,-l) if there is a 2-fold? Although I believe so...

What is "it"?

If you mean the tables in IDXREF.LP, they only report the fit of points
to a particular lattice.  They do not compare the intensities of 
potential symmetry mates.  Quoting from the program output:

  Note, that reflection integration is based only on orientation and metric
  of the lattice. It does not require knowledge of the correct space group!
  Thus, if no such information is provided by the user in XDS.INP,
  reflections are integrated assuming a triclinic reduced cell lattice;
  the space group is assigned automatically or by the user in the last
  step (CORRECT) when integrated intensities are available.

If you mean the output from a later run of pointless/aimless,
so far as I know it applies the symmetry operation being tested
to all reflections, which means that Friedel/Bijvoet pairs are 
not compared.  But I could be wrong on that point.

> And what is a good number? Is 20 % OK? What about 30 % and even higher?

Still refering to output from pointless/aimless, the crucial point is not
the absolute number but rather how the agreement for the symmetry operation
being tested compares to the agreement for the identity operation.

For example, here is the output for a lousy data set with a real 2-fold:

%
Scores for each symmetry element

Nelmt  Lklhd  Z-ccCCN  RmeasSymmetry & operator (in Lattice 
Cell)

  1   0.806   6.97   0.70   17852  0.516 identity
  2   0.919   7.67   0.77   21302  0.486 *** 2-fold k ( 0 1 0) {-h,k,-l}

[snip]

   Laue Group   Lklhd   NetZc  Zc+   Zc-CCCC-  Rmeas   R-  Delta 
ReindexOperator

 1  P 1 2/m 1  ***  0.919   7.30  7.30  0.00   0.73  0.00   0.50  0.00   0.1 
[-h,-l,-k]
 2   P -1   0.081  -0.69  6.97  7.67   0.70  0.77   0.52  0.49   0.0 
[h,-k,-l]
%%

In this case the program reports a 0.91 likelihood that the Laue
group is P2 even though the Rmeas is horrible.

Ethan

 
> Thanks a lot,
> Chen 
> 
> 
> > On May 13, 2015, at 6:07 PM, Ethan A Merritt  
> > wrote:
> > 
> >> On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote:
> >> Hi all,
> >> 
> >> I am sorry about this question which I should have figured out earlier. For
> >> point group determination, does the Rmeas consider Fridel pairs
> >> differently?
> > 
> > A Friedel pair consists of the [hkl] and [-h-k-l] reflections.
> > This pairing is independent of space group.
> > So the agreement or lack of agreement between Friedel pairs is
> > not informative about selection of point group or space group. 
> > 
> > You may be thinking of a Bijvoet pair, which consists of 
> > [hkl] and the Friedel mate of some symmetry equivalent of [hkl]
> > within a particular spacegroup.
> > 
> > But even in the presence of anomalous scattering I think that
> > Bijvoet pairs are expected to agree with each other better than
> > with a reflection not related by point group symmetry.
> > 
> >> (although I think it should be...) This is because I saw a
> >> derivative dataset collected at peak (from a demo) whose Rmeas is quite
> >> high (>50 %) for all the space groups tested (including P1). However, the
> >> native dataset has only <10 % Rmeas. Should I worry about the derivative
> >> dataset? There seems to be multiple lattices in both datasets based on
> >> IDXREF.
> >> 
> >> You inputs are really appreciated!
> >> 
> >> Sincerely,
> >> Chen
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] XDS Rmeas in space group determination

[Ethan A Merritt]

On Wednesday, 13 May, 2015 17:51:59 Chen Zhao wrote:
> Hi all,
> 
> I am sorry about this question which I should have figured out earlier. For
> point group determination, does the Rmeas consider Fridel pairs
> differently?

A Friedel pair consists of the [hkl] and [-h-k-l] reflections.
This pairing is independent of space group.
So the agreement or lack of agreement between Friedel pairs is
not informative about selection of point group or space group. 

You may be thinking of a Bijvoet pair, which consists of 
[hkl] and the Friedel mate of some symmetry equivalent of [hkl]
within a particular spacegroup.

But even in the presence of anomalous scattering I think that
Bijvoet pairs are expected to agree with each other better than
with a reflection not related by point group symmetry.

> (although I think it should be...) This is because I saw a
> derivative dataset collected at peak (from a demo) whose Rmeas is quite
> high (>50 %) for all the space groups tested (including P1). However, the
> native dataset has only <10 % Rmeas. Should I worry about the derivative
> dataset? There seems to be multiple lattices in both datasets based on
> IDXREF.
> 
> You inputs are really appreciated!
> 
> Sincerely,
> Chen
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] [RANT] Reject Papers describing non-open source software

[Ethan A Merritt]

gt;> Sent: Tuesday, May 12, 2015 20:40
> >> To: CCP4BB@JISCMAIL.AC.UK
> >> Subject: Re: [ccp4bb] [RANT] Reject Papers describing non-open source
> >> software
> >> 
> >> On May 12, 2015, at 12:29 PM, Roger Rowlett 
> >> wrote:
> >> 
> >>> Was the research publicly funded? If you receive funds from NSF, for
> > example,
> >> you are expected to share and "make widely available and usable" software
> >> and inventions created under a grant (section VI.D.4. of the Award and
> >> administration guide). I don't know how enforceable that clause is,
> > however.
> >> 
> >> The funding shouldn't matter. I suggest that a publication that has the
> > purpose
> >> of describing non-open source software should be summarily rejected by
> >> referees. In other words, the power is in our hands, not the NSF's.
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

[Ethan A Merritt]

On Thursday, 23 April, 2015 18:25:35 Gert Bange wrote:
> Dear Mishba,
> 
> Just check density vs model by simply open 'Coot',
> 
> Go to: 'File' -> 'Fetch PDB & Map using EDS'
> 
> Type the pdb entry into the field - enjoy the densities.

If you want to pursue the plausibility of specific outliers
you could also download and superimpose PDB entry 1LMB 
(deposited in 1993, 15 years earlier) and calculate a "Kleywegt plot"
comparing the difference in phi/psi between the two structures
at each residue they share. This is in the "validation" menu of Coot.

Compare the models at their points of difference and
decide for yourself.

1LMB has 0% phi/psi outliers, though it contains a smaller
piece of the structure. If you care to dig deeper,
you could re-refine 3BDN after substituting the 1LMB coordinates
for the 3BDN coordinates in the region where the chains
superimpose well.

I have not looked at any of the other related PDB structures,
but you would want investigate those as well.

Ethan



> 
> Best and god save the EDS,
> 
> Gert
> 
> 
> -
> LOEWE Center for Synthetic Microbiology
> AG Bange - Analysis of Metabolic Networks
> Dr. Gert Bange
> Hans-Meerwein-Strasse, C7
> 35043 Marburg, Germany
> office: +49-6421-28-23361
> fax: +49-6421-28-24430
> web: www.synmikro.com/bange
> -
> LOEWE Center for Synthetic Microbiology
> AG Bange - Analysis of Metabolic Networks
> Dr. Gert Bange
> Hans-Meerwein-Strasse, C7
> 35043 Marburg, Germany
> office: +49-6421-28-23361
> fax: +49-6421-28-24430
> web: www.synmikro.com/bange
> 
> 
> 
> Am 23.04.2015 um 18:03 schrieb Misbah ud Din Ahmad :
> 
> > Dear crystallographers, 
> > 
> > The PDB entry  
> > http://www.rcsb.org/pdb/explore.do?structureId=3BDN
> > has 16.5% Ramachandran outliers. When I opened this PDB file in coot and 
> > checked for Ramachandran outliers, the results are:
> > In preffered region: 58.04%
> > In allowed regions: 19.78%
> > Outliers: 22.17%  !
> > 
> > With an R-free of 37.4% at 3.9 A resolution, could you please tell me how 
> > reliable this structure of Lambda repressor bound to DNA is?
> > 
> > 
> > Thanks
> > Misbha
> > 
> > 
> > 
> >   
> >   
> > 
> > 
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] nVidia quadro Update for Linux

[Ethan A Merritt]

On Thursday, 02 April, 2015 23:47:12 mesters wrote:
> Great, so for stereo 10 to work under Linux you compiled a Linux kernel 
> built with USB device filesystem (usbfs) and USB 2.0 support?

usbfs was removed from linux starting with kernel version 3.5 (July 2012).
  
Some linux distros with "extended life" support for old kernels 
may still allow you to enable usbfs, but it's not a tenable requirement
going forward.  Whatever script or component was using this should
be updated to query /sys/kernel/debug/usb/...  instead.

Ethan

> 
> I see you did not implement the following, Option "3DVisionUSBPath" 
> "/sys/bus/usb/devices/1-1" , right?
> 
> Jeroen
> 
> Am 02.04.15 um 23:31 schrieb Lukasz Salwinski:
> > On 04/02/2015 02:05 PM, mesters wrote:
> >> After Kay send me an email today to have a look at the wiki at
> >> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo to 
> >> add my
> >> findings, I researched things further.
> >>
> >> I remember I wrote to the ccp4bb March 1st, 2013, asking about Nvidia 
> >> 3D Vision
> >> under Linux via USB/3-pin because back then for the first time 
> >> options for USB
> >> suggested this constellation might work under Linux as well. Nobody 
> >> could
> >> confirm it worked back then so I did not go for that option and 
> >> bought an ASUS
> >> VG278HR. But because monitors with build-in emitters are becoming 
> >> extinct, we/I
> >> need the alternative employing the Nvidia 3D Vision 2 glasses under 
> >> Linux I guess.
> >>
> >> Apparently this option is working, see
> >> http://cismm.cs.unc.edu/core-projects/visualization-and-analysis/setting-up-a-simple-stereo-system/
> >>  
> >>
> >>
> >> otherwise the following at Nvidia would not make much sense, see
> >>
> >> http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html /
> >> and
> >> ftp://download.nvidia.com/XFree86/Linux-x86/256.44/README/xconfigoptions.html
> >>  
> >>
> >> (search for USB and you will find it)
> >>
> >> So, I ask the question again, can somebody confirm the Nvidia 3D 
> >> Vision 2
> >> glasses with USB/3-pin now work under Linux? If so, I withdraw my 
> >> previous email.
> >>
> >> Jeroen
> >
> > See the attached snapshots. Both coot & pymol run happily in 3D
> > with nVidia emitter (hooked up through both USB and 3-pin cable)
> > and 3D vision 2 glasses.
> >
> > the relevant snippet of my xorg.conf reads:
> >
> > -
> > Section "Device"
> > Identifier "Device0"
> > Driver "nvidia"
> > VendorName "NVIDIA Corporation"
> > EndSection
> >
> > Section "Screen"
> > Identifier "Screen0"
> > Device "Device0"
> > Monitor"Monitor0"
> > DefaultDepth24
> > Option "UBB" "1"
> > Option "Stereo" "10"
> > Option "AllowDFPStereo" "1"
> > SubSection "Display"
> > Depth   24
> > EndSubSection
> > EndSection
> >
> > Section "Extensions"
> > Option "Composite" "Disable"
> > EndSection
> > --
> >
> >
> > cheers,
> > lukasz
> >
> >
> >
> >
> 
> 
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Fwd: Structure with high B-factor

[Ethan A Merritt]

On Tuesday, 17 March, 2015 17:34:24 Manish Shah wrote:
> Hi All,
> 
> I solved a structure using molecular replacement (Phaser) and the current
> R-factor and R-free is 0.2 and 0.25. The electron density looks great for
> residues and the ligand, however, the issue is with the B-values. The
> average B-value is 110 at this stage of refinement and I could not bring it
> down. All the residues are having a high B-values ranging from 90-120,
> while the R is good. I have tried several options in CCP4 (restrained
> refinement in Refmac) to bring it down and also used other MR programs, but
> still it still continues to be in the same range.
> 
> I will look forward to any suggestions. Thank you.

What was the Wilson B factor reported by Aimless or Truncate?
What is the resolution of the data?

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Basic Anomalous Scattering Theory

[Ethan A Merritt]

On Thursday, 12 March, 2015 10:41:46 Ethan A Merritt wrote:
> On Thursday, 12 March, 2015 13:11:10 Keller, Jacob wrote:
> > >If projects a middle-C-tone into a piano, do all of the lower notes 
> > >resonate as well, according to the Kramers-Kronig relation?
> >  If you press the right pedal  the harmonics of the note you play will 
> > resonate. My piano teachers never mentioned to me the  Kramers-Kronig 
> > relation but that's a long time ago, perhaps they do these days. 
> > 
> > Right, I always understood that it was just the harmonics which would 
> > resonate. But according to Kramers-Kronig, wouldn't there be resonance on 
> > all strings, just as there's anomalous scattering at all higher energies 
> > above the edge? Each string of lower frequency would be analogous to an 
> > anomalous scatterer with an edge at a lower energy than the incident 
> > radiation. Hmm, maybe it really does happen?
> 
> The better-known example is the precaution of having
> soldiers break step when crossing a bridge.  The higher-frequency
> input from march-tempo footsteps can excite a lower frequency 
> resonance in the bridge structure with possible bad consequence.

Note that this can lead to "anomalous scattering" of the incident soldiers.

Ethan


> But yes, it works for pianos too.
> 
>   Ethan
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Basic Anomalous Scattering Theory

[Ethan A Merritt]

On Thursday, 12 March, 2015 13:11:10 Keller, Jacob wrote:
> >If projects a middle-C-tone into a piano, do all of the lower notes resonate 
> >as well, according to the Kramers-Kronig relation?
>  If you press the right pedal  the harmonics of the note you play will 
> resonate. My piano teachers never mentioned to me the  Kramers-Kronig 
> relation but that's a long time ago, perhaps they do these days. 
> 
> Right, I always understood that it was just the harmonics which would 
> resonate. But according to Kramers-Kronig, wouldn't there be resonance on all 
> strings, just as there's anomalous scattering at all higher energies above 
> the edge? Each string of lower frequency would be analogous to an anomalous 
> scatterer with an edge at a lower energy than the incident radiation. Hmm, 
> maybe it really does happen?

The better-known example is the precaution of having
soldiers break step when crossing a bridge.  The higher-frequency
input from march-tempo footsteps can excite a lower frequency 
resonance in the bridge structure with possible bad consequence.
But yes, it works for pianos too.

Ethan




> A different question: do the real and imaginary components of anomalous 
> scattering arise from different processes, or are they simply a way to 
> represent the phase of the anomalous scattering?
> 
> All the best,
> 
> Jacob
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
> [kell...@janelia.hhmi.org]
> Sent: Wednesday, March 11, 2015 6:57 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Basic Anomalous Scattering Theory
> 
> Dear Crystallographers,
> 
> I have had only a vague understanding of what specific things are happening 
> with shell electrons at anomalous edges. Specifically, for example, to what 
> energy of electron-transition does the x-ray k-edge correspond in terms of 
> orbitals, and is that transition energy actually equal to the energy of the 
> photon, suggesting that the photon is absorbed (or disappears?) in elevating 
> the electron? I don't think we say it is absorbed, so how does the energy 
> come back out, from the electron's falling back down, right? So then there's 
> a new photon created, or the same one comes back out? Where was it?
> 
> Further, I also have heard that the emerging anomalous/resonance photons are 
> of the same wavelength as the incident radiation, but usually there is 
> something lost in transitions (even non-fluorescence ones) I thought? Has it 
> ever been definitively shown that the anomalous photons are of the same 
> energy as the incident radiation?
> 
> In the case of L-edges, why are there three separate edges? Further, if the 
> resonance occurs when the energies are equal, why does resonance occur at 
> energies greater than the edge? I don't think this happens in other resonance 
> phenomena, or does it? If projects a middle-C-tone into a piano, do all of 
> the lower notes resonate as well, according to the Kramers-Kronig relation? I 
> think it may actually happen in the mammalian cochlea's travelling wave, but 
> is it completely general to resonance phenomena?
> 
> Just interested, and have wondered these things for a long time in the 
> background of my mind...
> 
> Jacob Keller
> 
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Absence of contact between layers in a crystal

[Ethan A Merritt]

On Friday, 06 February, 2015 13:38:14 Rachel Kramer Green wrote:
> Dear CCP4BB users,
> 
> For additional information on this matter, please see:
> 
> wwPDB Statement on Retraction of PDB Entries
> http://www.wwpdb.org/documentation/UAB.php
> 
> and
> 
> Safeguarding the integrity of protein archive
> /Nature/ (2010) *463*:425. doi:10.1038/463425c 
> <http://www.nature.com/nature/journal/v463/n7280/full/463425c.html>
> 
> Sincerely,
> Rachel Green

Both of those statements are now 5 years out of date.
The linked URLs at UAB are now dead.  
The link to the US Office of Research Integrity works, but the
index to case summaries on that site has no listing for the Murthy affair
either as a closed or an open case investigation.

Furthermore the promised actions (retraction, obsolesence) apparently
never took place for whatever reason.  Can you provide an update?
Do you think that an open letter from the community would be helpful?


Ethan


> On 2/6/2015 7:35 AM, Mark van Raaij wrote:
> > In our structures 1H6W (1.9Å) and 1OCY (1.5Å) we observed something 
> > similar, I suspect the domain that makes the crystal contacts is 
> > three-fold disordered, leading to layers of nothing. In our paper in 
> > JMB 314, 1137 (doi 10.1006/jmbi.2000.5204) we tried to explain it a 
> > bit, and describe what was done to try and "show up" the missing domain.
> >
> > The 2HR0 structure was clearly made up, as were the data, apparently 
> > the mathematical function used to calculate the sigmas could be 
> > derived from the deposited data...It is indeed a pity that neither the 
> > structure nor the paper have been rejected. Perhaps the PDB is waiting 
> > for Nature, and Nature for the PDB...a joint letter to both might be 
> > in order to get this sorted out.
> >
> >
> > On 6 Feb 2015, at 11:58, Kerff Fred wrote:
> >
> >> Hello,
> >>
> >> Looking at structure 2HR0 ("The structure of complement C3b provides 
> >> insights into complement activation and regulation. »,Abdul Ajees, 
> >> A.,  Gunasekaran, K.,  Volanakis, J.E.,  Narayana, S.V.,  Kotwal, 
> >> G.J.,  Krishna Murthy, H.M.;  (2006) Nature 444: 221-225), I noticed 
> >> the absence of contacts between layers in the crystal. Is it 
> >> something that has already been observed in other crystals?
> >>
> >> Best regards,
> >>
> >> Fred
> >> -
> >> Frédéric Kerff
> >> Chercheur qualifié F.R.S.-FNRS
> >> Cristallographie des protéines
> >> Centre d'Ingénierie des Protéines
> >> Université de Liège
> >> 17, Allée du 6 Août - Bat B5a
> >> 4000 Liège (Belgium)
> >> Tel.: +32 (0)4 3663620
> >> Fax: +32 (0)4 3663772
> >>
> >>
> >>
> >>> Le 6 févr. 2015 à 10:12, Tim Gruene  >>> <mailto:t...@shelx.uni-ac.gwdg.de>> a écrit :
> >>>
> >>> -BEGIN PGP SIGNED MESSAGE-
> >>> Hash: SHA1
> >>>
> >>> Dear Smith,
> >>>
> >>> The sca file most likely does not contain flags. pointless can read
> >>> the sca file, standardise it to ccp4 standards and freerflag marks
> >>> random reflections. You should use the maximum of 500 unique
> >>> reflections or 5% of the unique reflections, whichever is larger.
> >>>
> >>> Best,
> >>> Tim
> >>>
> >>> On 02/06/2015 09:49 AM, Smith Lee wrote:
> >>>> Dear All, I have a sca file. Will you please tell me by which
> >>>> software or how I can know whether the sca file contains R-free
> >>>> tags? If not, by which software or how I can add the R-free tags?
> >>>> And how much of the reflections I add the R-free tags? I am looking
> >>>> forward to getting your reply. Smith
> >>>>
> >>>
> >>> - -- 
> >>> - --
> >>> Dr Tim Gruene
> >>> Institut fuer anorganische Chemie
> >>> Tammannstr. 4
> >>> D-37077 Goettingen
> >>>
> >>> GPG Key ID = A46BEE1A
> >>>
> >>> -BEGIN PGP SIGNATURE-
> >>> Version: GnuPG v1.4.12 (GNU/Linux)
> >>>
> >>> iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
> >>> j0JFZac4kAh8twpov71MG84=
> >>> =XN57
> >>> -END PGP SIGNATURE-
> >
> > Mark J van Raaij
> > Lab 20B
> > Dpto de Estructura de Macromoleculas
> > Centro Nacional de Biotecnologia - CSIC
> > c/Darwin 3
> > E-28049 Madrid, Spain
> > tel. (+34) 91 585 4616
> > http://www.cnb.csic.es/~mjvanraaij <http://www.cnb.csic.es/%7Emjvanraaij>
> >
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] How to apply NCS restraint to a ligand in refmac?

[Ethan A Merritt]

On Saturday, 31 January, 2015 00:51:08 Jurgen Bosch wrote:
> Hi Ethan,
> DM with a mask of the ligand in chain A then applying the NCS matrices and 
> looking at the resulting density perhaps ?

Real-space refinement is not the issue.
That can be done easily in Coot by calculating an NCS-averaged map
and then fitting the ligand into it.

I'm specifically interested in how to keep or introduce
the equivalent NCS restraint during subsequent refmac refinement.

> In Refmac you can also add a NCS restraint per residue - I assume a ligand is 
> considered a residue but I have not tried this.

Yes, but that doesn't actually help.
It restrains the ligand copies to look like each other internally,
but does not restrain their binding pose relative to the surrounding
protein.

    Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

[ccp4bb] How to apply NCS restraint to a ligand in refmac?

[Ethan A Merritt]

Is there some way to apply NCS restraints to the binding pose of a ligand
during refmac refinement?

That is, suppose I have 3 copies of the binding site and the density in
each copy is OK but not great.  I would be more confident of a refined
pose that jointly satisfied the electron density at all 3 sites than a
refinement that resulting in slightly different poses at each site. 

If not, is there an equivalent to the shelxl SAME directive?
I.e. is there a way to tell it "I don't know what the true 
distance is from ligand atom X to protein atom Y, but I want to restrain
it to be the same in all 3 copies"?

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Continuous-Single Versus Coarse-Multiple Sampling

[Ethan A Merritt]

On Friday, 23 January, 2015 20:36:08 Keller, Jacob wrote:
> No wikipedia link yet?

In practice the issue usually comes down to a consideration of the noise.
Is the noise systematic?  Is the signal/noise constant over time?  

If the noise is systematic, then repeated measurement of the same
data points will be biased by that systematic factor and will
overestimate the accuracy of the data.  This is an example of when
precision is distinct from accuracy. On the other hand this
protocol may allow you to better estimate and correct for a decrease
in signal/noise as a function of time.

Conversely spreading the measurement effort over a larger number
of points may result in a larger apparent sigma (lower precision)
but greater accuracy overall since the systematic effects are
more likely to be correctly identified as noise.

Relating this back to fine-slicing on phi, if the noise has a large
per-image component then fine-slicing is a bad idea because you 
increase the noise for no gain in signal.  On the other hand if
there is little or no per-image noise component, as is the case
for photon counting detectors, then fine-slicing potentially
decreases the noise because you do not have to estimate and subtract
the background from the portion of the time the reflection of 
interest does not intersect the Ewald sphere.

Ethan

> 
> JPK
> 
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
> Jacob
> Sent: Thursday, January 22, 2015 5:20 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Continuous-Single Versus Coarse-Multiple Sampling
> 
> Dear Crystallographers,
> 
> This is more general than crystallography, but has applications therein, 
> particularly in understanding fine phi-slicing.
> 
> The general question is:
> 
> Given one needs to collect data to fit parameters for a known function, and 
> given a limited total number of measurements, is it generally better to 
> measure a small group of points multiple times or to distribute each 
> individual measurement over the measureable extent of the function? I have a 
> strong intuition that it is the latter, but all errors being equal, it would 
> seem prima facie that both are equivalent. For example, a line (y = mx + b) 
> can be fit from two points. One could either measure the line at two points A 
> and B five times each for a total of 10 independent measurements, or measure 
> ten points evenly-spaced from A to B. Are these equivalent in terms of 
> fitting and information content or not? Which is better? Again, conjecture 
> and intuition suggest the evenly-spaced experiment is better, but I cannot 
> formulate or prove to myself why, yet.
> 
> The application of this to crystallography might be another reason that fine 
> phi-slicing (0.1 degrees * 3600 frames) is better than coarse (1 degree * 
> 3600 frames), even though the number of times one measures reflections is 
> tenfold higher in the second case (assuming no radiation damage). In the 
> first case, one never measures the same phi angle twice, but one does have 
> multiple measurements in a sense, i.e., of different parts of the same 
> reflection.
> 
> Yes, 3D profile-fitting may be a big reason fine phi-slicing works, but 
> beyond that, perhaps this sampling choice plays a role as well. Or maybe the 
> profile-fitting works so well precisely because of this diffuse-single type 
> of sampling rather than coarse-multiple sampling?
> 
> This general math/science concept must have been discussed somewhere--can 
> anyone point to where?
> 
> JPK
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Normal mode refinement

[Ethan A Merritt]

On Monday, 20 October, 2014 18:10:03 Appu kumar wrote:
> Dear CCP4 Users,
> I seek your valuable advice and suggestion in carrying out the normal mode
> structure refinement which manifest the dynamics of protein as linear
> combination of harmonic modes, used to describe the motion of protein
> structure in collective fashion. Studies suggest that it is highly useful
> in refining the protein structure which harbors a considerable magnitude of
> flexibility in atomic position owing to high thermal factors.
> Therefor I want to know is there any software/script available to execute
> the normal mode of refinement. Thanks a lot in advance for your imperative
> suggestions

The previously published examples of normal-mode refinement that I know
about used private external programs to generate thermal ellipsoids for each
atom, and then used those as fixed ADPs while refining coordinates in
refmac or similar standard program.  Again speaking only of the examples
I have looked at in detail, the result was "better" (had lower R factors)
than a conventional isotropic refinement but was not nearly as good as a
multi-group TLS refinement of the same structure (TLSMD + refmac).

On the other hand, there is a quite different way normal modes can be used
in refinement.   As I understand it (perhaps Garib will add addtional details)
the "jellybody" refinement mode of recent refmac versions can be viewed
as restraining the model shifts to be consistent with the principle normal mode.
In this way the normal mode contributes to the path of the refinement,
but is not explicitly part of the final model.  

So it may be that using TLSMD + refmac jellybody TLS refinement
would get you the best of both approaches, though I have not gone back
to look again at the published example structures since the advent of
jellybody refinement.  But note that jellybody is primarily useful when
you already have a high-qualityl, good geometry, starting model.

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] monitoring refmac refinement

[Ethan A Merritt]

On Thursday, 02 October, 2014 12:07:54 Alastair Fyfe wrote:
> I would be grateful for any advice on how to  obtain  refmac information 
> equivalent in detail to the shelxl "Disagreeable restraints before 
> cycle   N" listing. 

This is controlled by the MONI keyword.
To get a full list on every cycle
   MONI MANY


> In the later stages of refining a set of related 
> structures, I have been alternating between shelxl and refmac. Typically 
> this relies on  shelxl for occupancy assignment of alternate 
> conformations and associated partially occupied solvent, followed by 
> refmac on the shelxl result to improve bulk solvent modeling.  Most of 
> the time this two step approach works well and yields an  improvement in 
> the final model. However occasionally  the refmac step heads in the 
> opposite direction:
> 
>InitialFinal
> R factor0.1156   0.1390
>   R free0.1192   0.1477
>   Rms BondLength0.0108   0.0110
>Rms BondAngle1.3876   1.8731
>   Rms ChirVolume0.1147   0.0979
> 
> This seems to happen rather erratically relative to changes in the model 
> and I've been unable to determine which restraints/weights are responsible.
> Thanks for any pointers,
> Alastair Fyfe
> UCSC
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

[ccp4bb] ccp4 ligand tools + wwPDB validation = bug reports?

[Ethan A Merritt]

Earlier this year for the first time I got back a validation report from the
PDB for a deposited structure that included wwPDB validation of a ligand.
This is great stuff. I approve. I am happy.

Unfortunately the validation check reported problems with my ligand.
This is bad. I am unhappy.  What went wrong?

A long story follows.  Skip to the end for the TL;DNR summary.

Basically I am advocating to treat errors, omissions, or inadequacies
in the CCP4 ligand dictionaries as bugs in exactly the same sense
as program bugs.   Report them when you find them, get them fixed
in CCP4 updates, and down the road we will all have better structures.

 Long version 

Since last year I have been happily using the integrated tools Coot,
Jligand, cprodrg, and refmac5 to sketch a ligand, generate a dictionary,
fit to initial difference density, and refine.  In the absence of an independent
validation check, I thought everything was working acceptably.
The bad grade on my wwPDB validation report [pun intended] made 
me look into the guts of this tool chain more carefully trying to see
what went wrong.

In short here is what happens:

- coot fires up jligand

- I sketch the compound and click "accept"

- jligand creates a file prodrg-in.mdl that contains only
  atom type, connectivity, single/double bond flag

- cprodrg takes this and assigns each atom a more complete
  chemical label, for example
O  15.9994  CARBONYL OXYGEN (C=O)
CH2  12.011   ALIPHATIC CH2-GROUP
NR  14.0067  AROMATIC NITROGEN

- cprodrg then categorizes each bond by the assigned types of
  the two bonded atoms, and similarly categorizes each bond angle
  by the assigned types of its three constituent atoms.

So far so good.  Now comes the problematic part.

- cprodrg tries to find a target geometry (ideal bond length or angle)
  for each category by matching against the contents of the file
  .../Prodrg/param/ff/default
 If an exact match is not found, it falls through to ... well I'm not
 sure exactly what the rule is for falling through.  This is the part
 that goes wrong.

The content of this default parameter file is rather impoverished.
My ligand contained a pyrazole  (5-membered ring with 2 adjacent
nitrogens).  The nitrogens were assigned a category 
NR5  14.0067  NITROGEN (5-RING)
But the default file contains no bond or angle entries for this
atom type, so it "falls through" to the only N-N bond it does contain
NSP - NSP  target length 1.12Å
That's miles off, or at any rate more than 1/3 Å  off, the expected
length of 1.396Å tabulated in the Mogul database for a pyrazole.
(The wwPDB report listed a target of 1.37Å).

I don't expect perfection, but target errors of more than 0.3Å in
bond length are large compared to the expected accuracy of even
a modest resolution protein structure.  No wonder the wwPDB 
validation report flagged it as a 13 sigma outlier in the refined
structure.  

 TL;DNR version 

The $CCP4/share/prodrg/prodrg.param file does not contain
target values for many bond types that are correctly identified
by prodrg itself.

Adding a single line handling NR5-NR5 bonds to the source file 
ccp4-6.4.0/src/Prodrg/param/ff/default
yields a significant improvement in my refined protein structure.
Even the R/Rfree are improved, which surprised me.
These were identical runs except for the regenerated ligand dictionary.

Would it be appropriate to report this as a bug?I think so.

Where should I report it?

Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem

[Ethan A Merritt]

On Thursday, 12 June, 2014 20:24:43 Joel Tyndall wrote:
> Hi,
> 
> I saw Jeffs post with interest and have held off until now.  It is relatively 
> easy to find structures with bad geometry for small molecules but it does not 
> do any good simply pointing them out. What I believe is needed is a way to 
> fix the problem. There are several possible ways. The pdb could parse new 
> structures through a checking process to check the geometry of small 
> molecules. This, I would presume, could be done via the CSD.

As of January 2014 this is indeed being done as part of the PDB deposition 
process.

Anyone who has deposited a structure containing a ligand this year has 
probably been surprised, pleasantly or otherwise, by the table of geometry
violations/ouliers for each ligand.

If you missed the various announcements, you may wish to try it out on
your own structures here:

http://wwpdb-validation.wwpdb.org/validservice/


> I also believe that cif file generation can be improved.

Indeed.  All of the library-generation tools I am aware of are flawed in
their own idiosyncratic ways.   I think I shall start a campaign to treat
errors in the cif libraries as "bugs", and encourage people to report
these bugs in the libraries we all use just as they do for bugs in the
programs we all use.  

Ethan


> The developers of the available programs are doing a great job but as 
> intelligent scientists we strive for perfection. I am unfortunately not in a 
> position to develop software myself ( so maybe I should pipe down) but I 
> would be happy to offer assistance (from my personal experience). In my 
> experience I have had some issues with small molecule parametrisation ( or 
> maybe I just deal with unusual molecules). By that I mean, on occasion I have 
> had a .cif files that simply do not make sense or contradicts what you would  
> expect in the geometry of a small molecule. I am aware of one "service" that 
> does check against the CSD when generating cif files.
> 
> I read in one of the editorials, or related posts that one of the structures 
> was corrected. This is also an option assuming the data has been deposited.
> 
> My two cents
> 
> J
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim 
> Gruene
> Sent: Friday, 13 June 2014 5:54 a.m.
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem
> 
> Hi Jeff,
> 
> there are quite a few implications in your brief email that each might open a 
> long thread of discussion. As brief as possible I think one has to be a good 
> scientist and a good crystallographier to fully understand the meaning of a 
> crystal structure, and I think many people believe a crystal structure is 
> just a set of coordinates.
> 
> If someone tells me some distance in yards and I assume that's about the same 
> as a meter I will surely get some dodgy results up to creating the first car 
> accident on Mars ;-)
> 
> Cheers,
> Tim
> 
> On 06/12/2014 07:04 PM, Jeffrey Bell wrote:
> > Hi, Tim,
> > 
> > Thanks for your comment. Do you agree with the editorial's claim that some 
> > 25% of the deposited protein-ligand complexes might be dodgy in significant 
> > details? 
> > 
> > 
> > This editorial comment represents something that I often hear from drug 
> > discovery professionals. Is it a matter of PR between crystallographers and 
> > other scientists, or does a real problem exist?
> > 
> > Cheers,
> > 
> > Jeff Bell
> > PrimeX developer
> > Schrödinger, Inc.
> > 
> > 
> > On Tuesday, June 10, 2014 10:27 AM, Tim Gruene  
> > wrote:
> >  
> > 
> > 
> > I hope that the contents of this section is obvious to most readers of 
> > the ccp4 bulletin board.
> > 
> > Cheer,
> > Tim
> > 
> > 
> > On 06/10/2014 03:40 PM, Jeffrey Bell wrote:
> >> An editorial comment about protein crystallography appeared under 
> >> that title. It's short and worth considering.
> >> http://pipeline.corante.com/
> > 
> > 
> > 
> 
> --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] EDSTATS for an extracted fragment

[Ethan A Merritt]

On Wednesday, 11 June, 2014 20:01:45 Gerard DVD Kleywegt wrote:
> > What you want is a test for how well each model agrees with its own map. It 
> > is fair to argue that the model that is more self-consistent (agrees better 
> > with its own map) is the better model.  But you won't learn that by 
> > comparing model A to map B.
> 
> However, conversely, if your modified model fits the original map better than 
> the model that was used to calculate the map itself, you've done a good bit 
> of 
> model building. 

But the current context is a question about using EDSTATS, which asks for a
difference map as part of evaluating the fit.

If the fit of the original model is bad, its difference map is going to be
polluted by both positive and negative peaks.  Any nearby residues
will get a bad score.

Now suppose you somehow have a new model that is perfect.
If you try to score the new model using that same map, those same
difference peaks are still present (obviously) and the nearby residues
in the new model will also get a bad score even though they are 
blameless in that they wouldn't have generated any difference peaks
themselves, being "perfect".

So far as I can see, it never makes sense to score model A based
on a difference map generated from model B.

Ethan

> If you want to do this calculation (with all the warnings and 
> caveats), you can also use MAPMAN - 
> http://xray.bmc.uu.se/usf/mapman_man.html#S41 . The method you propose is 
> essentially the same as this one: http://www.ncbi.nlm.nih.gov/pubmed/18598022 
> but for a fragment of your macromolecule instead of for a ligand (if you 
> don't 
> have access to the journal, you can request a reprint here: 
> http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=87 )
> 
> --Gerard
> 
> **
> Gerard J. Kleywegt
> 
>http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> **
> The opinions in this message are fictional.  Any similarity
> to actual opinions, living or dead, is purely coincidental.
> **
> Little known gastromathematical curiosity: let "z" be the
> radius and "a" the thickness of a pizza. Then the volume
>  of that pizza is equal to pi*z*z*a !
> **
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] EDSTATS for an extracted fragment

[Ethan A Merritt]

On Tuesday, 10 June, 2014 19:13:57 George Devaniranjan wrote:
> Thank you Ian.
> To clarify,  I actually want to compare the new PDB file to the old MTZ
> file to see how well the residues fit. This is why I mentioned that I have
> the old MTZ file I generated from SF's which I got from the PDB.
> 
> I am not trying to improve the deposited structure, I am trying to get a
> metric of how "bad" the residues become if I change certain residue phi and
> psi values when I fit into the original electron density.

That is not a valid test.  The old map resulted from refinement of the
old model, and it corresponds to phases that are only correct for that
same old model.   If you perturb the model you will of course get a
different map, but "different" != "bad".  The old model won't agree 
with your new map and the new model won't agree with the old map.
That doesn't prove that either the old model or the new model is
better or worse.

What you want is a test for how well each model agrees with its own map.
It is fair to argue that the model that is more self-consistent
(agrees better with its own map) is the better model.  But you won't learn that
by comparing model A to map B.

Caveat:  This all assumes that the map phases are generated entirely
from the model.  If you have a map generated from experimental phases,
then it certainly makes sense to ask which of several models is in better
agreement with the experimental map.

cheers,

Ethan


> 
> 
> 
> On Tue, Jun 10, 2014 at 5:55 PM, Ian Tickle  wrote:
> 
> > Hi, sorry small clarification.
> >
> > The "complete PDB file that you used to run the refinement job" (i.e. the
> > input PDB file) will obviously only be suitable in the case that you did 0
> > cycles of refinement.  If you did some refinement of the model then the
> > co-ordinates will have changed, and then you need the _output_ PDB file
> > from that refinement as input to EDSTATS (clearly if you did 0 cycles the
> > input and output PDB files from the refinement will be the same & it
> > doesn't matter which one you use).
> >
> > Cheers
> >
> > -- Ian
> >
> >
> > On 10 June 2014 21:46, Ian Tickle  wrote:
> >
> >>
> >> Hi, I'm puzzled by what you are trying to do.  You say you have the
> >> original MTZ/MAP files.  What have the original files got to do with it?
> >> EDSTATS requires the MTZ/MAP file calculated for the supplied model.  The
> >> documentation states: "... the PDB file and the maps should all be from
> >> the same refinement job.".  The refinement job referred to could be 0
> >> cycles but the MTZ file must have been calculated from the PDB file
> >> supplied.  If you have changed the PDB file then the original MTZ/MAP files
> >> will no longer be suitable.  This means you have to supply exactly the same
> >> complete PDB file that you used to run the refinement job.
> >>
> >> Cheers
> >>
> >> -- Ian
> >>
> >>
> >> On 10 June 2014 19:52, George Devaniranjan 
> >> wrote:
> >>
> >>> HI,
> >>>
> >>>
> >>> I want to calculate real-space R factor/RSCC and such parameters using
> >>> EDSTATS in CCP4 but only for a selected fragment that has been
> >>> extracted and then modified (changed the Phi and Psi) from the native.
> >>>
> >>>
> >>> I have the original MTZ and MAP.
> >>>
> >>>
> >>> Is it even possible to calculate these values without inserting the
> >>> extracted fragment back into the rest of the PDB (the unmodified part)?
> >>>
> >>>
> >>> I am reluctant to do that since I have many such fragments I have
> >>> extracted and modified and wish to compare with the native.
> >>>
> >>>
> >>> Thank you,
> >>>
> >>> George
> >>>
> >>
> >>
> >
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Bfactors too high after TLS refinement

[Ethan A Merritt]

On Thursday, 05 June, 2014 17:51:33 Carles Palanca i García wrote:
> 
>   P { margin-bottom: 0.21cm; }
> 
> 
> Hello,
> 
> I'm almost done refining a protein-DNA
> complex at 3A, but when I apply TLS (Refmac+TLSanl to include the
> ANISOU component) the B factors increase from 50-60 to 100-110 A2.
> The crystal is a bit special since it has 80% of solvent and the
> Wilson B-factor is 87 A2. When I compare my Bfactors with other
> structures of similar resolution using Phenix Validation, my data is
> clearly an outlier.
> 
> 
> To perform the TLS refinement I have
> generated .tlsin files for 2,4 and 6 groups with the TLSmd server and
> used them in refmac jobs consisting of 20 cycles of TLS refinement+50
> cycles of restrained refinement. This way the R-factor and R-free
> values have drop 1-2% (before it was 22.3/24.1). The three different
> options suffer from the same problem regarding high B-factors after
> TLSanl. Am I doing something wrong during the TLS refinement? What
> can I do to preserve the original Bfactors?

Preserving the original B factors should not be your goal.
I can explain part of what you are seeing, but probably not the
entire effect.

When you refine using TLS, the various programs convert this back
to an "equivalent isotropic B factor".  Sometimes this is marked by
the programs as "Beq", but it is placed in your output PDB
file simple as "B" with no warning that it is only an approximation.

But not only is Beq an approximation, it is invariably an overestimate of
the isotropic B.   Beq can run as much as 40% larger than
the "true" isotropic B.  A better estimate Best is available but so far
as I know none of the standard programs use it.   Math, charts, and
example demonstrations of the too-large Beq are reported in

 "Some Beq are more equivalent than others". Acta Cryst. A67, 512-516. 
 E. A. Merritt (2011). 

Ethan




> 
> 
> Thanks in advance,
> 
> Carles Palanca.
> 
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Observations-to-parameter ratio in Refmac

[Ethan A Merritt]

On Tuesday, 03 June, 2014 17:02:56 Klaus Fütterer wrote:

> Does someone know whether Refmac outputs the observations-to-parameters ratio 
> or, failing that, the number of refined parameters in the log file? 
> 
> Klaus

This turns out to be much more complex than you might think.
See:

  "To B or not to B: a question of resolution?" Acta Cryst. D68, 468-477.
http://scripts.iucr.org/cgi-bin/paper?S0907444911028320

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Ethan A Merritt]

On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
> As long as it's just a Technical Comments section - an obvious concern 
> would be the signal/noise in the comments themselves.  I'm sure PDB 
> would not relish having to moderate that lot.
> 
> Alternatively PDB can overtly link to papers that discuss technical 
> issues that reference the particular structure - wrong or fraudulent 
> structures are often associated with refereed publications that point 
> that out, and structures with significant errors often show up in that 
> way too.  I once did a journal club on Muller (2013) Acta Cryst 
> F69:1071-1076 and wish that could be associated with the relevant PDB 
> file(s).

Perhaps some combination of those two ideas?

The PDB could associate with each deposited structure  a crowd-sourced
list of published articles citing it. They already make an effort to
attach the primary citation, but so far as I know there is currently
no effort to track subsequent citations.   

While spam comments in a free-format forum are probably inevitable,
spam submission of citing papers seems less likely to be a problem.

- Ethan

> > On Wed, May 14, 2014 at 12:32 PM, Zachary Wood  > <mailto:z...@bmb.uga.edu>> wrote:
> >
> > Hello All,
> >
> > Instead of placing the additional burden of policing on the good
> > people at the PDB, perhaps the entry page for each structure could
> > contain a comments section. Then the community could point out
> > serious concerns for the less informed users. At least that will
> > give users some warning in the case of particularly worrisome
> > structures. The authors of course could still reply to defend their
> > structure, and it may encourage some people to even correct their
> > errors.
> >
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] High B-factors

[Ethan A Merritt]

On Tuesday, 13 May, 2014 22:49:15 Kgosisejo, Oarabile wrote:
> Hi all,
> 
> We have solved the structure of a protein at 2.3 A with the final R-work and 
> R-free at 0.24 and 0.28, respectively. However, the B-factors are high, with 
> an average of 72. There are 3 molecules in the asymmetric unit and the 3rd 
> molecule is very disordered and I believe is the main contributor to high 
> B-factors.
> 
> Also is there a way I can improve the B-factors of my model?

The first thing I suggest is to check what is the Wilson B from your data 
processing.
If the data intensity distribution already indicates that the expected mean B 
is high,
then I wouldn't worry about it.

You could then test whether the high B factors are due to bulk motion of the 
molecules
rather than disorder or large motions of individual residues.  Do this by 
placing each
chain into a single TLS group and refining the structure again in the presence 
of this
3-group TLS model. 

> I was wondering if there is a way I can look at the B-factors of the 
> molecules individually. 

If you do go ahead and refine a 3-group TLS model, you can feed it to the 
server at
http://skuld.bmsc.washington.edu/parvati/
Among other things, it will create a nice picture of your 3 chains colored by
B factor.

Ethan


> 
> Best Regards,
> 
> Oarabile Kgosisejo
> 
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] EDS server - R-value

[Ethan A Merritt]

On Friday, 04 April, 2014 10:44:18 Nat Echols wrote:
> On Fri, Apr 4, 2014 at 10:39 AM, Alastair Fyfe  wrote:
> 
> > Reconstructing the refinement may be necessary in some cases but  there
> > are other applications (pdb-wide map statistics, development of map
> > analysis tools, quick model vs map checks) where access to the depositor's
> > final map would be sufficient.
> 
> I think these kinds of bulk analyses will be less effective if the maps are
> not calculated consistently.  For instance, the question of how to handle
> missing reflections can make a big difference.
> 
> Perhaps the coefficients are in fact included in many of the available
> > mmCIF  files? I should check..
> >
> 
> No, because most of those mmCIF files were probably converted from MTZ
> format by the deposition server(s).

I think depositing map coefficients is the wrong way to go.

Better to deposit the Fcalc along with the Fobs (or Iobs as you prefer)
and people can make maps using whatever set of coefficients they want.

Last time I checked a random sample of PDB entries, about half of
them provided Fcalc.   I think it should be added to the "mandatory" 
category of deposition information.

Ethan

Re: [ccp4bb] SO4 geometry

[Ethan A Merritt]

On Monday, 31 March, 2014 19:01:33 Oganesyan, Vaheh wrote:
> Colleagues,
> 
> Sorry to bother for something really minor. The Refmac usually always 
> recognizes tetrahedral SO4 groups and there were no problems related to its 
> geometry. Two attached files demonstrate SO4 geometry before and after 
> refinement. Would you be able to point me to mistake I’m doing?


Apart from any question of geometry, I conclude from the
B factors >> 100  that refmac doesn't think the sulfate belongs there.

As to geometry - the refmac log file should contain mention of whatever
target was problematic.  I would guess that the chiral volume has the
wrong sign.

Ethan


> Thank you.
> 
> Regards,
> 
> Vaheh Oganesyan, PhD

Re: [ccp4bb] Coot Performance on Intel HD Graphics 5000

[Ethan A Merritt]

On Friday, 28 March, 2014 12:35:57 mesters wrote:
> The OpenGL performance is rather poor on intel HD chips up to and 
> including the HD 4600 

My experience differs.  
I have not seen dramatically different performance in practice between coot
running on nvidia and the same program version running on Intel HD4000. 
Yes the OpenGL benchmarks are radically different, but that doesn't seem
to reflect what is acheived by programs of interest.  I notice more of a
difference in Pymol performance, but not such a huge difference as to be a
problem.

> but with the appearance of HD 5000 series (Iris 
> HD) the Cinebench OpenGL score increased dramatically and even 
> challenges many nvidia cards in performance. With these kind of intel 
> chips you should be able to run Coot and Pymol smoothly and operate a 
> passive 3D screen without problems.
> 
> HOWEVER
> 
> Good 2-core chips would be Core i5-4258U 
>  or Core i5-4288U 
>  with plenty of performance and, no 
> surprice, found in many Apple computers (not the mini model, too 
> bad...). Have not yet seen one mini-pc with these chips but this is 
> probably due to need for active (and sometimes loud) cooling.
> One mini PC with a 4-core and Iris Pro Graphics is the new Gigabyte Brix 
> Pro. Already the model with the "low end" chip Core i5-4570R 
>  is EXTREMELY loud.

I'm running a fanless i7-3517UE (Ivy Bridge).  Totally silent.

Ethan

> 
> Even the NUC D54250WYKH with the fast 2-core i5-4250U becomes VERY VERY 
> noisy during "video" demanding operations (tested by Hardware). The NUC 
> DN2820FYKH with the celeron chip and HD 5000 is the only quiet model but 
> very slow otherwise (intended for video playback at home).
> 
> All in all, a choise between big, fast, full with air and quiet (good 
> old desktop) or, small and very noisy (D54250WYKH) or, small, quiet and 
> slow (DN2820FYKH) or, the smallest but expensive iMac (so no box on your 
> desk) with the i5-4250U (no other all-in-one PCs with Iris Pro)..
> 
> - Jeroen -
> 
> 
> Am 27.03.14 19:25, schrieb Dale Tronrud:
> > -BEGIN PGP SIGNED MESSAGE-
> > Hash: SHA1
> >
> > Hi all,
> >
> > My lab desktop PC broke and I'm looking into replacements.  Being
> > tired of the enormous tower (full of air) occupying much of my desk
> > I looking at systems like the Intel NUC.  These systems are too small
> > for video cards so I'd be working with the integrated Intel graphics.
> > Is the 5000 version of their graphics good enough for Coot to work
> > nice?  I am not interested in stereo.
> >
> > Dale Tronrud
> > -BEGIN PGP SIGNATURE-
> > Version: GnuPG v2.0.22 (MingW32)
> > Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
> >
> > iEYEARECAAYFAlM0bRwACgkQU5C0gGfAG11raACgrYltSYvIbVrVVLHxMfMPgfyn
> > MJEAn1i2cUEedyXeYOtjIAw7HvAB2qeL
> > =YIfi
> > -END PGP SIGNATURE-
> 
> 
> 

Re: [ccp4bb] Weird MR result

[Ethan A Merritt]

On Thursday, 14 November, 2013 18:58:27 Niu Tou wrote:
> Dear Phil,
> 
> I used PHASER to do the task. I have double checked and  both files have
> the same prefix, so they are from the same output. I have also checked the
> headers again, they have the same spacegroup. Actually I was trying to
> search for two different molecules but only one was found. The spacegeoup
> is P2 and I am quite sure it is not P21 from system absence.

P21 is 100 times more common than P2.
There are only 160 protein structures in P2 in all of the PDB

So although it is of course possible for it to be P2, it is more likely from
a priori expectations to be P21 with "prohibited" large intensities for the
0k0 relections.  You definitely need to consider P21 as a possibility
when running MR.

Ethan


> 
> One possibility is that the space group was wrong, since there is a 95% off
> origin peak. There are several choices from data processing, P1, P2, C2
> C222, all have this large off origin peak. I wonder if this 95% peak can
> tell some information?
> 
> It will not surprise me if this result is incorrect, however how could
> these regular density be?
> 
> Best,
> Niu
> 
> 
> On Thu, Nov 14, 2013 at 5:47 PM, Phil Jeffrey wrote:
> 
> > Hello Niu,
> >
> > 1.  We need extra information.  What program did you use ?  What's the
> > similarity (e.g. % identity) of your model.  What's your space group ? Did
> > you try ALL the space groups in your point group in ALL the permutations
> > (e.g. in primitive orthorhombic there are 8 possibilities).
> >
> > 1a.  My best guess on limited info is that you've got a partial solution
> > in the wrong space group with only part of the molecules at their correct
> > position.
> >
> > 2.  I recently had a very unusual case where I could solve a structure in
> > EITHER P41212 or P43212 with similar statistics, but that I would see
> > interpenetrating electron density for a second, partial occupancy molecule
> > no matter which of these space groups I tried (and it showed this when I
> > expanded the data to P1).  Might conceivably be a 2:1 enantiomorphic twin,
> > in retrospect, but we obtained a more friendly crystal form.  I hope you
> > don't have something like that, but it's possible.
> >
> > Phil Jeffrey
> > Princeton
> >
> >
> > On 11/14/13 5:22 PM, Niu Tou wrote:
> >
> >> Dear All,
> >>
> >> I have a strange MR case which do not know how to interpret, I wonder if
> >> any one had similar experiences.
> >>
> >> The output model does not fit into the map at all, as shown in picture
> >> 1, however the map still looks good in part regions. From picture 2 we
> >> can see even clear alpha helix. I guess this could not be due to some
> >> random density, and I have tried to do MR with a irrelevant model
> >> without producing such kind of regular secondary structure.
> >>
> >> This data has a long c axis, and in most parts the density are still not
> >> interpretable. I do not know if this is a good starting point. Could any
> >> one give some suggestions? Many thanks!
> >>
> >> Best,
> >> Niu
> >>
> >>
> >>
> >

Re: [ccp4bb] Problematic PDBs

[Ethan A Merritt]

On Thursday, 17 October, 2013 10:51:08 Lucas wrote:
> Dear all,
> 
> I've been lecturing in a structural bioinformatics course where graduate
> students (always consisting of people without crystallography background to
> that point) are expected to understand the basics on how x-ray structures
> are obtained, so that they know what they are using in their bioinformatics
> projects. Practices include letting them manually build a segment from an
> excellent map and also using Coot to check problems in not so good
> structures.
> 
> I wonder if there's a list of problematic structures somewhere that I could
> use for that practice?

4KAP is a nice cautionary example of failing to properly refine a ligand
after placement.   

- Open coot, download 4KAP + map from EDS.  
- Navigate to ligand and view difference density map.   
- Oops.
- Now open up residue information for the ligand.  Notice anything odd?

For bonus points, look up the known ligation chemistry of this site.
Notice that the binding pose of the 4KAP ligand does not match it.

Ethan

> Apart from a few ones I'm aware of because of (bad)
> publicity, what I usually do is an advanced search on PDB for entries with
> poor resolution and bound ligands, then checking then manually, hopefully
> finding some examples of creative map interpretation. But it would be nice
> to have specific examples for each thing that can go wrong in a PDB
> construction.
> 
> Best regards,
> Lucas

Re: [ccp4bb] how to cut back resolution of a well-refined model

[Ethan A Merritt]

On Thursday, 10 October, 2013 22:44:34 Jim Pflugrath wrote:
> Please tell me why Rpim should be looked at.  Cannot one have meaningless 
> data and have lots of multiplicity to drive Rpim lower without any real 
> benefit?  Under what conditions is Rpim useful?


> And suppose one looks at  (and not /) and CC1/2.  What of it?
> 
> And let me write what Phil wrote in a slightly different way:
> Please explain how you think that adding the resolution from 2.6 A to 2.45 A 
> will improve your model.

That's an easy one.

Extending the resolution from 2.6Å to 2.45Å will increase the number of
observations  by about 1/3.  Even aside from the fact that these 
contributions are adding information at higher resolution,  simply the
increased number of unique observations is expected to make your refinement
more robust and improve the parameter estimates that make up your model.

Ah, you say, but what if all those additional observations are all noise?
That's where the inspection of I/sig(I) offers some guidance.
In this particular case we are told that at 2.45Å the mean I/sig(I) is still > 
2.
So at least in this case these are definitely not all noise.

Ethan

 
> Sorry, but maybe it is too soon after the last CC1/2 discussion to raise 
> these points, but I am truly interested in various opinions about all this.

 
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Gerard 
> Bricogne [g...@globalphasing.com]
> Sent: Thursday, October 10, 2013 5:28 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] how to cut back resolution of a well-refined model
> 
> Dear Yafang,
> 
>  Is it the case that you collected these data on a Pilatus detector,
> using relatively low exposure and high multiplicity? These types of datasets
> always give what looks like alarmingly high values of R-merge, and many
> people who are set in their ways (like so many reviewers still are) tend to
> conclude that the alarm is about the data being bad, whereas it is about
> Rmerge being a terrible statistic in these situations. The Rpim statistic,
> on the other hand, is the one to look at if you want an R-like quantity, and
> it is well behaved in this regime. Of course, look at CC1/2 as well, and
> I/sigI as you did.
> 
> 
>  With best wishes,
> 
>   Gerard.
> 
> --
> On Thu, Oct 10, 2013 at 04:57:20PM -0400, Yafang Chen wrote:
> > Hi All,
> >
> > I have a structure at 2.45A which has been well refined. However, since the
> > R-merge at the last shell is above 1 (although I/sigmaI at the last shell
> > is more than 2), we now decide to cut back the resolution to about 2.6A. Is
> > there a way to do this based on the well-refined model instead of doing the
> > MR and refinement all over again? Thank you so much for your help!
> >
> > Best,
> > Yafang
> >
> > --
> > Yafang Chen
> >
> > Graduate Research Assistant
> > Mesecar Lab
> > Department of Biological Sciences
> > Purdue University
> > Hockmeyer Hall of Structural Biology
> > 240 S. Martin Jischke Drive
> > West Lafayette, IN 47907
> 
> --
> 
>  ===
>  * *
>  * Gerard Bricogne g...@globalphasing.com  *
>  * *
>  * Global Phasing Ltd. *
>  * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
>  * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
>  * *
>  ===
>

Re: [ccp4bb] Fwd: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21

[Ethan A Merritt]

On Wednesday, 02 October, 2013 17:31:06 wtempel wrote:
> Tim,
> I agree with your statement.
> Consider this situation:
> Macromolecular sample MA produces crystal CA. Data scale well in C2221 and
> refinement proceeds smoothly to give stuctural model SA.
> Slightly modified macromolecular sample MA* crystallizes to yield crystal
> CA*. Data scale well in C2221 with cell dimensions virtually identical to
> those of CA. I attempt, without spatial transformation, to solve the
> structure by refining SA using CA* data and for each HKL in CA* assign the
> same flag value as in same HKL of CA. I am not aware of any alternative
> equivalent indexing issue in this space group and am surprised to learn
> that SA does not refine well against data from CA*, Rfree does not drop
> from 48%, while Rcryst drops from 46 to 44%. Modifying SA to better
> correspond to MA* does not help. I scale data from CA* in P21. Over 10
> cycles of refinement, Rcryst, Rfree drop from 35 -> 29%, 34 -> 33%. As I
> assigned a new Rfree set, I am not surprised about Rfree < Rcryst,
> initially. Neither does the modest reduction in Rfree convince me that
> symmetry reduction yielded a true improvement in the model. 

If I understand correctly, your starting Rfree (prior to refinement) was
48% if the model was placed in a C2221 cell and 34% if the same model
was placed in a P21 cell.   That seems more than a "modest reduction".

However, based solely on your description above it remains a formal 
possibility  that the CA* structure really is orthorhombic but is not
isomorphous to the CA structure even though the two unit cells are
virtually identical. Perhaps the molecule sits differently in the asymmetric
unit.  Did you try treating it as a fresh molecular replacement problem?

Ethan




> For that
> purpose, I would prefer a comparison of refinement in C2221 and P21 with
> properly transfered free flags. I just do not know how to accomplish that
> transfer.
> W.
> 
> -- Forwarded message --
> From: Tim Gruene 
> Date: Wed, Oct 2, 2013 at 4:13 PM
> Subject: Re: [ccp4bb] Fwd: [ccp4bb] expanding reflections from C2221 to P21
> To: wtempel 
> Cc: CCP4BB@jiscmail.ac.uk
> 
> 
> Dear W.,
> 
> if P21 is a proper subgroup of C2221, scaling a P21 data set in C2221
> would try to make non-equivalent reflections equal, would it not? I
> would reintegrate the data in the correct point group and scale in the
> correct space group.
> 
> Best,
> Tim
> 
> On 10/02/2013 08:32 PM, wtempel wrote:
> > Hello Appu and Boaz, my suspicion arises from failure to refine (as
> > in reducing crystallographic R-factor from the 40%s) a related,
> > virtually isomorphous crystal structure in the original C2221
> > setting. Scaling statistics are very nice even in C2221. If I drop
> > the symmetry to P21, the R-factor drops to a little more than 0.3
> > and the maps look significantly cleaner. Caveat: because I am not
> > using a consistent free set between the C2221 and P21 settings, I
> > do not trust Rfree as a reliable progress indicator in this case.
> > P21 is a subgroup (or superset) of C2221, per "the tables". And as
> > there is a transformation between them, should not that
> > transformation be applicable to the "lattice sampling"? I would
> > therefore like to cleanly expand my free set from C2221 to P21.
> > Using REINDEX following Appu's suggestion, with specification of
> > the new space group again gets me the familiar P21 cell dimensions,
> > but the unique reflection count remains unchanged when I would
> > expect it to approximately double. Now I do not know how to best
> > generate the other half of the data set or even if something is
> > wrong at this point already. W.
> >
> > -- Forwarded message -- From: Appu kumar
> >  Date: Wed, Oct 2, 2013 at 1:29 PM Subject:
> > Re: [ccp4bb] expanding reflections from C2221 to P21 To: wtempel
> > , CCP4BB 
> >
> >
> > How do you suspect that C2221 is 'pseudo' and P21 is 'real'? You
> > can use the reindex programme incorporated in ccp4 suit. Reindex
> > programme can expand symmetry from C2221 to P21.I Hope you will get
> > the result. Thank you Appu
> >
> >
> > On 2 October 2013 21:43, wtempel  wrote:
> >
> >> Hello, I would like to expand a reflection data set in mtz format
> >> from C2221 to P21. The purpose is to obtain consistent R-free
> >> flags based on a structure already refined in C2221 for a related
> >> data set that I suspect is pseudo-C2221 but "real" P21.
> >>
> >> Primitive cell dimensions are: 37.6 126.1 40.61 89.99 117.6
> >> 90.01, C-centered: 37.6 71.99 126.1 90 89.99 90.01 pointless
> >> provides the following matrix:  Reindex operator from
> >> input cell to lattice cell: [h,h+2l,-k]
> >>
> >> h'   = ( h k l ) (   1   1   0 ) (   0   0
> >> -1 ) (   0   2   0 )
> >>
> >>  In sftools, I loaded the C2221 data set and did
> >>
> >> sftools$ reindex matrix 1 0 0 0 0 -1 -.5 .5 0
> >>
> >> with the transposed (to account fo

Re: [ccp4bb] tricky mr problem

[Ethan A Merritt]

On Monday, 23 September, 2013 22:01:32 RHYS GRINTER wrote:
> Hi all,
> 
> I have been attempting to find a MR solution for a low resolution data set 
> (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel 
> I'm working on.
> 
> I've created a trimmed poly-alanine from a structure of 17% identity, that 
> gives a solution with a Tfz of 14.3 with two molecules per asu (llg is around 
> 900). I'm guessing this in a genuine solution, but the map is too poor to 
> build into.
> 
> Does anyone have any advice as to proceed from here? It may be just a case of 
> needing better resolution data to work with, but would this indicate that 
> Selenomet derivative crystals won't be needed for this structure?

Apart from whether you "need" SeMet for phasing, when you are having trouble 
fitting into
poor maps it can help a lot to have the location of methionines pinned down by 
peaks
in an anomalous difference Fourier map.

Ethan

Re: [ccp4bb] Off-topic, visualization

[Ethan A Merritt]

On Thursday, 05 September, 2013 23:17:09 Folmer Fredslund wrote:
> If you play around with the settings you can do something similar 
[in pymol]
> http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#cut
> 
> mvh
> Folmer

For what it's worth, I note that Raster3D differs from most/all of the other
programs in that it allows you to slice through any arbitrary plane.
The plane is defined by three points (usually a choice of 3 atoms
for convenience).

Pymol and (I think) the others only allow you to clip against a plane that
is normal to the screen, tied to a single clipping value along Z.
That is, you cannot rotate the sliced object to view the same slice from
some other angle.

Ethan


> 
> 2013/9/5 Ethan A Merritt 
> 
> > On Thursday, 05 September, 2013 13:30:21 Arthur Glasfeld wrote:
> > > I am hoping to create some images of protein cross-sections where the
> > atoms are depicted as spheres, and the spheres that are "cut" by the slab
> > are shown as solids with the same color as the surface.  An example of what
> > I'm after can be found here:
> > >
> > > people.reed.edu/~glasfeld/xsection.jpg
> > >
> > > Does anyone know of any software that can produce similar images?
> >
> > http://skuld.bmsc.washington.edu/raster3d/raster3d.html
> >
> >
> > >
> > > Thanks,
> > >
> > > Arthur Glasfeld
> > > Reed College
> > > Portland, OR
> >
> 
> 
> 
> 

Re: [ccp4bb] Off-topic, visualization

[Ethan A Merritt]

On Thursday, 05 September, 2013 13:30:21 Arthur Glasfeld wrote:
> I am hoping to create some images of protein cross-sections where the atoms 
> are depicted as spheres, and the spheres that are "cut" by the slab are shown 
> as solids with the same color as the surface.  An example of what I'm after 
> can be found here:
> 
> people.reed.edu/~glasfeld/xsection.jpg
> 
> Does anyone know of any software that can produce similar images?  

http://skuld.bmsc.washington.edu/raster3d/raster3d.html


> 
> Thanks,
> 
> Arthur Glasfeld
> Reed College
> Portland, OR

Re: [ccp4bb] Off-topic: PDB statistics

[Ethan A Merritt]

On Mon, 15 Apr 2013, Raji Edayathumangalam wrote:


Hi Folks,
Does anyone know of an accurate way to mine the PDB for what percent of total 
X-ray structures deposited as on date were done using molecular replacement? I
got hold of a pie chart for the same from my Google search for 2006 but I'd 
like to get hold of the most current statistics, if possible. The PDB has all 
kinds
of statistics but not one with numbers or precent of X-ray structures deposited 
sorted by various phasing types or X-ray structure determination methods.

For example, an "Advanced Search" on the PDB site pulls up the following:

Total current structures by X-ray: 78960
48666 by MR

5139 by MAD

5672 by SAD

1172 by MIR

94 by MIR (when the word is completely spelled out)

75 by SIR
5 by SIR (when the word is completely spelled out)
That leaves about 19,000 X-ray structures either solved by other phasing 
methods (seems unlikely) or somehow unaccounted for in the way I am searching. 
Maybe
the way I am doing the searches is no good. Does someone have a better way to 
do this?


There is no way to tell the PDB  "I already had phases for this structure 
because
it's just a soak or co-crystallization of a new ligand in a well-studied crystal
form."  Sometimes those are labeled as "MR" sometimes "isomorphous" sometimes 
some other string no label at all.  I have tried annotating such depositions as

"known structure" but it gets changed to something else.  Anyhow I could easily
believe there are 19000 of these.

 Ethan





Thanks much.
Raji

--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Against Method (R)

[Ethan A Merritt]

On Wed, 27 Oct 2010, Frank von Delft wrote:


So, since the experimental error is only a minor contribution to the total
error, it is arguably inappropriate to use it as a weight for each hkl.

I think your logic has run off the track.  The experimental error is an
appropriate weight for the Fobs(hkl) because that is indeed the error
for that observation.  This is true independent of errors in the model.
If you improve the model, that does not magically change the accuracy
of the data.

Sorry, still missing something:

In the weighted Rfactor, we're weighting by the 1/sig**2 (right?)  And the 
reason for that is, presumably, that when we add a term (Fo-Fc) but the Fo is 
crap (huge sigma), we need to ensure we don't add very much of it -- so we 
divide the term by the huge sigma.


Correct.

But what if Fc also is crap?  Which it patently is:  it's not even within 20% 
of Fo, never mind vaguely within sig(Fo).  Why should we not be 
down-weighting those terms as well?


Because here we want the exact opposite.  If Fc is hugely different from a
well-measured Fobs then it is a sensitive indicator of a problem with the model.
Why would we want to down-weight it? 
Consider the extreme case:  if you down-weight all reflections for which Fc does

not already agree with Fo, then you will always conclude that the current model,
no matter what random drawer you pulled it from, is in fine shape.

Or can we ignore that because, since all terms are crap, we'd simply be 
down-weighting the entire Rw by a lot, and we'd be doing it for the Rw of 
both models we're comparing, so they'd cancel out when we take the ratio 
Rw1/Rw2?


Not sure I follow this.

But if we're so happy to fudge away the huge gorilla in the room, why would 
we need to be religious about the little gnats on the floor (the sig(Fo))? 
Is there then really a difference between R1/R2 and Rw1/Rw2, for all 
practical purposes?


Yes.  That was the message of the 1970 Ford & Rollet paper that Ian provided a
link for.

 Ethan


(Of course, this is all for the ongoing case we don't know how to model the 
R-factor gap.  And no, I haven't played with actual numbers...)


phx.

Re: [ccp4bb] cross-section view of (protein) molecules in pymol?

[Ethan A Merritt]

On Friday 13 March 2009, Jacob Wong wrote:
> Dear all,
> http://www.nature.com/nature/journal/v458/n7234/fig_tab/nature07819_F3.html
> 
> Just came across this figure Fig. 3b) and would like to know what is the
> general and easiest way to make things like this, as a "non-brainer". Thank
> you, -Jacob

I don't know of any way to not engage a brain in the process,
but that particular figure could be made by
1) create electrostatic coloured surface in GRASP or MSMS or 
2) export surface as a file and convert it to Raster3D
3) define a bounding plane (some point on the plane + a surface normal)
4) render the surface in Raster3D, clipped by the bounding plane

Example:   top figure in
  http://skuld.bmsc.washington.edu/raster3d/examples/examples.html


I have been slowly working to put together a less brain-involving
pathway,  ideally involving some smallish number of mouse clicks in 
Coot or PyMol or ccp4mg that feed the information to Raster3D for rendering.
But nothing is currently in place that would allow a label
"no actual brains were consumed in producing this figure".

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] TLS refinement

[Ethan A Merritt]

On Tuesday 03 March 2009, Nalam, Madhavi wrote:
> Hello:
> I am trying to refine a structure at 3 A resolution using TLS refinement. 
> After 8-10 cycles of TLS refinement, R-free and R-factor converges. But 
> R-free starts going up again from the first round of restrained refinement. 
> My question now is can I stop just after TLS refinement without doing any 
> restrained refinement? 

In the "Refinement Parameters" panel of the ccp4i interface to refmac5, select
'refine _overall_ temperature factors' rather than 'refine _isotropic_ 
temperature factors'.


> If so, the PDB file contains ANISOU cards for the atoms. Does this mean 
> anisotropic refinement is performed on the atoms which should not be the case 
> for a 3 A structure? 

No.  The ANISOU records contain the Uij approximation to the result of applying
your TLS model to each atom.



> Thanks in advance,
> Regards,
> Madhavi
>  
> 
> 
> 
> From: CCP4 bulletin board on behalf of Edward A. Berry
> Sent: Tue 3/3/2009 5:39 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] shape complementarity calculations - oops!
> 
> 
> 
> Oganesyan, Vaheh wrote:
> 
> > Among non-runnable programs in CCP4 there is the sc program that indeed
> > does not run.
> >
> 
> Sorry, I didn't see the rest of your post.
> I had sc running and producing meaningful results back in 2006-2007,
> I can check which version etc.
> 
> Ed
> 
> 
> 
> 



-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] scaling a SAD data set

[Ethan A Merritt]

On Monday 02 February 2009, Vesna Serrano wrote:
> Dear all,
> I have a problem with a SAD data set. My crystal is very sensitive to
> radiation damage, so I have collected 2 110 frame data sets, 180 deg
> apart. I have processed the data with HKL2000 and it turns out that the 2
> sets have very different scales. My question is whether it would be
> possible to normalize the scales for these two data sets, so that I can
> use anomalous information in order to localize the anomalous scatterer in
> my structure.

You would do better to go back to the unscaled data, and feed the
unmerged intensities from both datasets into the SAD phasing program.
Let it do the scaling jointly.

Better yet would have been to collect the data in smaller wedges using
"inverse beam mode".

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] structure (factor) amplitude

[Ethan A Merritt]

On Saturday 10 January 2009, Bernhard Rupp wrote:
> Dear All,
> 
> I am getting conflicting comments on the use of 
> 'structure factor amplitude'
> vs. just
> 'structure amplitude'
> for |F|.

???
That's just... odd.

|F| is the amplitude of F.
But no way F is a "structure".


-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

[ccp4bb] A primer on linux shared libs [was: ccp4-6.1.0: iMosflm libtermcap.so.2 error - SOLVED]

[Ethan A Merritt]

>Maybe the version that comes with ccp4 6.1.0 was, in my case, a buggy one??
> 
> 
> 
>Until next time
> 
> 
> 
>Thanks again
> 
> 
> 
>Victor Alves
> 
> 
> 
> 
> 
>  Quoting "Johan P. Turkenburg" :
> 
> > Hi,
> >
> > You can use the website at packages.ubuntu.com to search for this file
> > in the contents (!) of the packages available for Entrepid.
> >
> > For libtermcap.so it tells you to install libncurses5-dev
> >
> > Install this using synaptic (the package manager).
> >
> > You may then have to create a link for libtermcap.so.2 by going to
> > /usr/lib/ (I assume that's where it will be installed) and doing
> > ln -s libtermcap.so libtermcap.so.2
> >
> > I can't test this, as I have decided to keep the LTS Hardy Heron.
> >
> > HTH
> >
> > Johan
> >
> >
> > Victor Alves wrote:
> >> Greetings
> >>
> >> And you say: - "Oh no! It's him again..."
> >>
> >> I know ... and even promised William Scott (in a private email) to   
> >> not bother you again until Christmas, but...
> >>
> >> First question: is CCP4BB the proper channel for these questions   
> >> and doubts? Or should I email directly the developers?
> >>
> >> As I said, this is a new laptop with a 32bits Ubuntu Intrepid Ibex   
> >> 8.10 and a fresh new installation of ccp4 6.1.0.
> >>
> >> When I open iMosflm (whether from within the ccp4i or from the   
> >> command line" I get an window with the following error message:
> >>
> >> iMosflm 1.0.0, 16th October 2008 (requiring Mosflm 7.0.4)
> >>
> >> iMosflm cannot run "usr/local/xtal/ccp4/ccp4-6.1.0/bin/ipmosflm":
> >>
> >> /usr/local/xtal/ccp4/ccp4-6.1.0/bin/ipmosflm: error while loading   
> >> shared libraries: libtermcap.so.2: cannot open shared object file:   
> >> No such file or directory
> >>
> >> Please configure iMosflm with the correct executable.
> >>
> >> I searched for libtermcap.so.2 and couldn't find it in my computer.
> >>
> >> Help please and thank you
> >>
> >> Victor Alves
> >>
> >>
> >>
> >> 
> >> This message was sent using IMP, the Internet Messaging Program.
> 
> 
> 
> 
> This message was sent using IMP, the Internet Messaging Program.
> 



-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Depositing coordinates with riding hydrogens

[Ethan A Merritt]

On Thursday 18 December 2008, Ed Pozharski wrote:
> > > Riding hydrogens are *not* part of your model, 
> > 
> > The fact that you don't see H in your fo-fc map due to limited
> > resolution and high level of noise does not mean that H atoms are not
> > present in actual real structure -:)
> > 
> 
> Let me ask you this - are bond length restraints part of the *model*?
> Obviously not, they are part of refinement target.  In the same way
> riding hydrogens are used to calculate the refinement target, but they
> do not increase the number of parameters of your model.  So I guess my
> definition of the "model" excludes deduced parameters.

The riding-hydrogen treatment is definitely part of the model.
But the number of parameters associated with it is not derived from the
number of individual hydrogen atoms and their coordinates, it is
limited to the number of parameters needed to describe the riding model
itself.  I.e. what is the C-H bond length and assigned geometry for 
each class of C and N atom for which hydrogens are generated.
On the order of a dozen parameters total, I would guess, though I have
not inspected this part of the code in refmac.
 
> > Not all programs and their versions place H atoms the exact same way
> > (using same geometry values, same rules for B-factors assignment: in
> > some programs H inherit the B-factors of the atom it's attached to, in
> > some it is multiplied by the factor from 1.1... to 1.5, etc. What
> > about occupancies, especially for alternate conformations?).
> > 
> But as I said, (if) the program and version is included in the PDB file,
> riding hydrogens can always be reconstructed.  

If you can find that particular version of the program!

This is relevant also for regenerating the treatment of bulk
solvent, particularly if a mask is involved.  The K/B values for 
a bulk solvent model stored in the PDB header records are not sufficient
by themselves to reproduce the calculation made by a particular program.

Perhaps there should be a registry of the parameters associated with
each version of each refinement program, and the PDB file could refer
to the appropriate parameter set by name rather than including it 
in-line in each individual PDB entry.


-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer?

[Ethan A Merritt]

On Thursday 11 December 2008, Santarsiero, Bernard D. wrote:
> In parallel with the discussion around this off-CCP4-topic, are they any
> good examples of the opposite case, where the protein is a monomer in
> solution (as evident from light scattering, MW determination through
> centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer?

I don't think such a question is entirely well-defined, for two reasons.

1) The monomer/dimer equilibrium in solution may well depend on the specific
   conditions (pH, concentration, presence of ligands, temperature, etc).
   Unless these conditions are replicated in your crystallization medium,
   it is uncertain to what extent the solution measurement is relevant.

2) How extensive an interface is required in order for it to be considered
   a dimer/multimer interaction?   In the limiting case of very small 
   interfaces, the entire crystal might be consider a single oligomer,
   with each lattice-packing contact constituting a monomer:monomer
   interaction.  That's not a very useful place to set the threshold,
   but where do you set it - 100 A^2 ?  500 A^2 ? 1000 A^2?
   Some definition other than surface area?

That said, I have some interest in the question as a practical matter.
We have a new structure that is "obviously", but totally unexpectedly,
a tetramer in the crystal.  In this case the monomer:monomer interaction
surface is >1500 A^2. But exactly what criteria would I use to
argue that this is a real tetramer?  What criteria would I use to
argue that it is a crystal artifact?   Yes, of course ideally one would
go back to the lab and survey for solution measurements that are 
consistent with tetramerization, but that is not always practical,
and may lead right back to your original question.


-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] RNA Torsion Angle Measurement Error

[Ethan A Merritt]

On Friday 28 November 2008, Donnie Berkholz wrote:
> On 16:04 Fri 28 Nov , Ethan A Merritt wrote:
> > On Friday 28 November 2008, Ben Akiyama wrote:
> > > I am measuring and comparing torsion angles in several solved 
> > > crystal structures of RNA helices using AMIGOS. I was wondering if 
> > > anyone knows of a program that can give me an idea of the error in 
> > > these measurements based on coordinate error, b-factors, etc.
> > 
> > If you mean real torsion angles, the only quantitative way to do this 
> > is to do full-matrix refinement, invert the matrix, and derive error 
> > estimates from the off-diagonal terms.  That is not something you can 
> > do after the fact from a previously refined structure.
> 
> I'm trying to answer a related question right now. Does anyone have a 
> good feeling for how this method would compare with 

> (1) propagated error from the coordinate esu and also with 

In order to propagate error estimates from individual ADPs and atomic
coordinates, you have to assume that the errors are independent.
But they are not.  Consider the real-life scenario of a flexible loop
refined using the usual set of crystallographic restraints.  The 
uncertainty in the atomic position is large, and probably the ADPs
are large to match.  But the error/uncertainty in bond lengths and
angles are not so large, because they have been restrained during
refinement.  That is, the whole loop and all the atoms in it may flop 
2A to one side or to the other, but the restraints prevent the CA from
flopping 2A to one side while CB flops 2A to the other.
Conversely, since their are no restraints on the torsion angles,
their uncertainty may be if anything underestimated by error propagation.
 
> (2) repeated refinements using randomized coordinates against the same data 
> set?

I suspect that it depends on the data quality, and on the individual structure.
But since it is easy to conduct the experiment, why not try it out on
your protein refinement of interest? 

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] RNA Torsion Angle Measurement Error

[Ethan A Merritt]

On Friday 28 November 2008, Ben Akiyama wrote:
> Hi Everyone,
> 
> I am measuring and comparing torsion angles in several solved crystal 
> structures of RNA helices using AMIGOS. I was wondering if anyone knows 
> of a program that can give me an idea of the error in these measurements 
> based on coordinate error, b-factors, etc.

If you mean real torsion angles, the only quantitative way to do this is
to do full-matrix refinement, invert the matrix, and derive error estimates
from the off-diagonal terms.  That is not something you can do after the
fact from a previously refined structure.

On the other hand, perhaps you can provide more information about what
exactly is the question you want to answer.

For example, if you are interested in how reliable the assignment of sugar
puckers is, looking at torsion angles is not a good way to go about this.
I think you'd be better off counting satisfied/unsatisfied hydrogen bonding
partners for the ring oxygens.

Also, your mention of AMIGOS throws me off a bit.  That program
calculates a pseudo-atom simplified representation of the model, right?
If you are asking about the pseudo-torsion angles associated with
pseudo-atoms, then I think there are no actual "measurements" directly
associated with them in the first place.  Perhaps the paper describing
AMIGOS discusses the issue of how sensitive the simplified representation
is to small variation in the original coordinates?  That's actually
an interesting question, but I don't have any intuitive feel for the answer.


-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Program to fill unitcell randomly

[Ethan A Merritt]

On Friday 28 November 2008, Mueller, Juergen-Joachim wrote:
> 
> Dear all,
> does anybody know a program to
> fill an unit cell a,b,c randomly by an arbitrary number
> of spheres (atoms)?

First you would need to define "random".
 Uniform density throughout the lattice?
 Uniform distribution of neighbor-neighbor distances?
 Uniform fractional coodinates?
 Must the placement conform to space group symmetry?

It is probably impossible to satisfy all of the above jointly.

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Choosing TLS groups.

[Ethan A Merritt]

On Thursday 13 November 2008, Pavel Afonine wrote:
> Hi Ian,
> 
> > All - I was just in a discussion about TLS and one thing that came out
> > that I hadn't been aware of is that for the Biso restraints Refmac
> > restrains the difference between the 'residual' Bs, i.e. with the TLS
> > contributions subtracted, not the 'total' Bs.  Now it seems to me that
> > this isn't quite correct, because it's the total motion of the atoms
> > that matters, i.e. the total mean square along-bond displacements for
> > bonded atoms should be equal.  However, I can see that in practical
> > terms it won't make any significant difference provided appropriate
> > precautions are taken with the choice of TLS groups.
> >   
> 
> given the formula for total atomic B-factor:
> 
> Btotal = Bcryst + Btls + Blocal + ...
> 
> my naive understanding is that the B-factors describing local atomic 
> vibrations Blocal (or residual B-factors as named in Refmac) should obey 
> Hirshfeld's "rigid-bond test" (Acta Cryst. (1976). A32, 239-244), which 
> is (to some approximation) enforced by the  restraints applied to 
> "residual" B-factors (as it is Refmac or in phenix.refine).

It makes perfect sense to apply the restraints to the residual B
_within_ a TLS group.  Furthermore, the along-bond variance from the
Btls component is zero for atoms within the group anyhow (by definition).
So for two atoms in the same TLS group, applying the restraint to the
total is numerically identical to applying it to the residual B only.

But this doesn't address Ian's concern about discontinuities across
a group boundary.  If two neighboring atoms are in different TLS groups,
then the along-bond variance from the two Btls components is different.
Hence in this case the _total_ B should be restrained.

> I think given the arbitrariness (or accuracy if you like) in defining 
> TLS groups, applying similarity restraints to the total B would not be a 
> good idea. 

I do not follow you thinking on that point.  If restraining the total
B is a good idea in the usual refinement protocol, either isotropic or
anisotropic, in how would it suddenly become not a good idea in
the presence of a TLS-based protocol?

The TLS description is not "truth". It is a convenient model that allows
us to predict (or explain) the ADP for each atom. Because it is only a
model, not truth, we should restrain it to conform to our prior knowledge.
In this particular case the prior expectation is that the net ADPs
of adjacent atoms are compatible, which means that their along-bond
components should be equal.  Therefore it only makes sense to apply the
restraint to the net ADP.

Think of it like this.  The same formulae which express the "restraint"
also express the extent to which the current model deviates from our
ideal for a "good" model.  If I hand you a refined model, you can
calculate this deviation from goodness without even a hint as to
how I arrived at that model.  It might have been Biso only, it might
have been TLS, it might have been a random drawing of B values from
a large hat.  Doesn't matter.  The same is true if you apply the
restraint during refinement;  if it's a good restraint, it's good 
regardless of how your model B factors are generated.

> I faced this dilemma a few years ago when implementing TLS  
> refinement in phenix.refine. And to prove my feelings and make a 
> decision, I systematically tried both possibilities, and the best result 
> was to apply the restraints to residual B-factors. 

I hesitate to suggest it, but...
might this be pointing to a coding error rather than to a flaw in the
rationale?  

> The NCS restraints are applied to residual B-factors too
> (although I didn't test it systematically).

Applyinig NCS restraints to B factors is a whole separate area
for discussion. Let's not go there just now :-)

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] half occupancy question-further information

[Ethan A Merritt]

On Saturday 18 October 2008, Leoanrd M Thomas wrote:
> To clarify a bit, the protein is not cyclic, it is two of the wild type
> protein molecules joined together by a short peptide linker creating a
> "new" protein.
> 
> Here is my attempt at an ascii sketch,
> 
>   2-fold 2-fold
> __
>(  )(  ) Linker
>   ()  ()
>  (  )(  )
>  (  )(  )
>   ()  ()
> Linker (__)(  )
> 
> When looking at the crystal imagine half the unit cells of the crystal
> have the linker on the "bottom" of the protein and the other half have it
> on the top.

Your description seems to contain the answer to your question.
Since half of the time the linker is in one place, and half of the time
it is in the other place, then that is what you should describe and refine.
Place the linker in both places in the model, but at half occupancy.
The fact that the linker spans two asymmetric units is not relevant.

We have refined systems that were very similar to your case,
where bi-functional ligands bound with one end on one protein molecule
and the other end on a different protein molecule, spanning two
asymmetric units. We had the further complication that the specific
ligand binding sites on the two multimeric protein molecules were not 
crystallographically equivalent.

> The modified protein crystallizes in the same space group and 
> unit cell as the wild type.
> 
> I am just not sure how to describe it or for that matter refine the
> system.  One half of the new molecule is in the ASU while the other half
> is related by the crystallographic two fold.
> 
> We have run the usual checks for twining and making sure we are in the
> proper space group.  We would not have this problem if we ignored the
> higher symmetry, of course it would be wrong.  It refines nicely in both
> the space groups but the overall processing statistics really indicate
> that it is in the higher space group.
> 
> Cheers,
> Len
> 
> 
> 
> Leonard M. Thomas Ph.D.
> Director, Macromolecular Crystallography Laboratory
> Howard Hughes Medical Institute
> California Institute of Technology
> Division of Biology
> 1200 E. California Blvd.  MC 114-96
> Pasadena, CA 91125
> 626-395-2453
> [EMAIL PROTECTED]
> http://www.br.caltech.edu/cmclab
> 



-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] high tempterature factor refinement problem

[Ethan A Merritt]

On Friday 17 October 2008, Carl Soja wrote:
> Hi All,
> 
> I just refined a structure at 2.95A and getting a good R-work and
> R-free(0.236 and 0.274). When I checked the PDB, I found many  residues have
> high temperature factor over 100. How can I use Phenix or CNS fix those high
> temperature factor for further refinment?

By "fix", do you mean "correct" or do you mean "not refine"?

The high average value is quite possibly correct already,
but it is true that you should probably not be refining individual
B factors at that resolution.

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] Off topic: GPU accelerated crystallographic calculations

[Ethan A Merritt]

On Thursday 18 September 2008, Andrzej Lyskowski wrote:
>   I was just testing CUDA enabled version of VMD and saw an increase of 
> calculation speed just like promised - more or less 70 times!
> 
>   Makes me wonder is anybody writing crystallographic software plans to 
> implement GPU support for the calculations? It would be nice to use all 
> the resources of our computers.

During the many years I have been using computers for crystallography,
I have seen repeated cycles of a leap-frog race between specialized
hardware and faster general-purpose CPUs.  As you point out, we are
currently in a cycle where customizing your code to offload certain
computations to a GPU can increase the overall throughput.  At least
for crystallographic software, previous iterations of this leap-frogging
have shown that such code customization is quite expensive in development
time while yielding only a short-lived advantage over general-purpose
code run on general-purpose hardware.  For instance, there was a period
in the late 1980s when you could improve your refinement time by buying
machines with separate vector array processors (Convex, FPS, probably
others I have forgotten).  But it was only a few years before cheaper
general-purpose machines leap-frogged back into the lead.  I am dubious
that averaged over a 5-year period the investment in specialized code
development and expensive specialized hardware was a net win.

And indeed, here is a recent harbinger that the era of GPU-based
computation may be very short-lived:
  http://arstechnica.com/articles/paedia/gpu-sweeney-interview.ars


A similar alternation has been seen historically in the tradeoff between 
self-contained platforms and external computational resources accessed
by relatively dumb terminals.  For some years now computer use has
favored self-contained laptops or graphics workstations.  But now the 
pendulum is swinging back again. Yeah, it's a bit different this time.
This time around the external resource is distributed ("cloud computing")
rather than centralized, but in essence it's "déjà vu all over again".
Whether the cloud computing fad will extend to crystallography remains
to be seen.  Note that distributed ("cloud") data storage has been
seriously proposed as a possible solution to the problem of archiving raw
diffraction images.

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742