Re: [ccp4bb] Coot crashes when delete side chain

[Chris Langendorf]

Hi Jinhua,

Following on from Mike's great tip, if you do forget to tick the "Keep
Delete Active" dialog box and your coot window crashes, you can recover
your old session.  After coot crashes, open a new coot window and go to
"File" then "Save Coordinates", a new dialogue box pops up asking to
"Select Filename", click on that and your old (crashed) session will open
back up in a new window, the side chain will also be deleted! You can now
close the superfluous new coot session. I don't know why this works, just
glad that it does :)

Chris

On Wed, 8 Mar 2023 at 09:47, Michael Gorman <
9a16aac7520c-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Jinhua,
> A temporary fix to the problem I have seen is to tick the 'Keep Delete
> Active' dialog box. Strange, but I'm sure Paul will come up with a fix soon.
> HTH
> Mike
>
> On Wednesday, 8 March 2023, 09:11:08 am AEDT, Wu, Jinhua <
> jinhua...@fccc.edu> wrote:
>
>
> Hi all,
>
>
>
> I recently upgraded my iMac to a 6-Core Intel i5 running Ventura 13.2.1. I
> installed Coot 0.9.8.7 together with CCP4. Now every time when I select
> delete sidechain (or sidechain zone) and click on the residue, Coot
> crashes. Does anyone have the same problem or know the solution to this
> issue?
>
>
>
> Thanks,
>
> Jinhua
>
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[ccp4bb] 27th Annual SCSB Structural Biology Symposium - Registration NOW OPEN

[White, Mark]

You and your colleagues are cordially invited to join us for the

27th Annual Structural Biology Symposium

to be held on

April 29, 2023

in Levin Hall, UTMB Galveston.

The meeting is organized by the Sealy Center for Structural Biology & Molecular 
Biophysics and co-sponsored by the Keck Center for Computational & Structural 
Biology. This year’s speakers include:


Yunfeng Chen Ph.D. Univ. of Texas Medical Branch

Ruben L. Gonzalez Jr., Ph.D. Columbia University

John A. Tainer, Ph.D. University of Texas MD Anderson Cancer Center

David W. Taylor, Ph.D. University of Texas

Junjie Zhang Ph.D. Texas A University


To register or for more information, visit https://scsb.utmb.edu/symposium


Mark Andrew White, Ph.D.
Associate Professor of Biochemistry & Molecular Biology,
UTMB, Galveston, TX
409.747.4747
https://xray.utmb.edu




























































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[ccp4bb] Postodoc position in RNA biophysics & structural biology

[ENNIFAR Eric (ARN)]

1 POSTDOC POSITION IN RNA BIOLOGY, BIOPHYSICS AND STRUCTURAL BIOLOGY 

We are hiring 1 postdoc (Servier laboratories funding, 2 years) 
Candidate should have good knowledge and possibly expertise in RNA Biology 
(chemical probing would be a plus), as well as expertise or strong knowledge in 
biophysics and/or structural biology (NMR, X-ray crystallography, possibly 
cryoEM). Our projects are related to non-coding RNAs involved in cancers, 
neurodegenerative diseases and emerging RNA viruses. 
Our group « Structure & Dynamics of Molecular Machines » is made up of 6 CNRS & 
INSERM scientists + 3 CNRS IR engineers, with complementary skills in molecular 
biology, biochemistry, biophysics, X-ray crystallography, NMR, cryoEM, 
Molecular Dynamics. 

Place: Institut de Biologie Moléculaire et Cellulaire - IBMC, Strasbourg 
(France) 
Lab "Architecture et Réactivité de l'ARN" 
contact: Eric Ennifar ( e.enni...@unistra.fr ) 
Deadline: April 24th 



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[ccp4bb] Research Software Scientist for the Data Group in Macromolecular Crystallography

[Kate Smith]

Dear Colleagues from the CCP4bb,

The Paul Scherrer Institute is looking for a Research Software Scientist to 
join the macromolecular crystallography (MX) Data group at the Swiss Light 
Source (SLS).

Your tasks
You will expand and develop Python packages to analyze data from scientific 
instruments, not only for traditional MX experiments but also for new 
techniques currently being developed at the MX beamlines for SLS 2.0 and 
SwissFEL. Participate in the commissioning of new beamline instruments together 
with beamline scientists and engineers. Contribute to strategic planning for a 
cutting-edge and sustainable software framework. Publish results in scientific 
journals and present at international conferences.

Your profile
- You will be qualified to PhD level in natural science or a related field.
- You have experience in using Python to answer scientific questions.
- You have good communication skills, with a personal interest or experience in 
working at the boundary between computing and science.
- You are fluent in English (spoken and written). A working knowledge of German 
would be advantageous.

For more information & to apply, please visit: 
https://www.psi.ch/en/pa/job-opportunities/56218-research-software-scientist

Please submit your application online by 30 March 2023.

Best regards,

Kate

--

Dr Kate Mary Louise Smith
MX Data - Software Developer
Swiss Light Source 
Paul Scherrer Institut
tel: +41 56 310 2128
email: kate.sm...@psi.ch



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Re: [ccp4bb] To Trim or Not to To Trim

[Harry Powell]

Whoops!

A quick glance at the PDB entry indicates I must have been clairvoyant to have 
read it 20 years ago. 

Harry

> On 20 Mar 2023, at 10:35, Harry Powell  wrote:
> 
> And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or 
> not cramin is a protein, since it has “only” 46 amino acids) where (from 
> memory, I haven’t read the paper for at least 20 nyears…) they modelled 
> multiple water networks.
> 
> 3NIR, for reference.
> 
> Harry
> 
> 
>> On 20 Mar 2023, at 10:20, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Thank you for such a careful analysis of modelling a "true" structure. You 
>> should publish this James.
>> 
>> It shows amongst other things, how R factors depend on our modelling of 
>> solvent which is not represented as individual atoms (And also I think on 
>> how the scales are derived between observation and calculation.)
>> Years ago someone refined vitamin B12 against high resolution (0.6A?) data. 
>> There is about 20-25% solvent volume I think..t was clear in the maps that 
>> there were partially occupied networks of water which extended throughout 
>> the lattice. This is probably true for proteins as well, and must affect the 
>> conformations of surface sidechains? 
>> Eleanor
>> The B12creference ...
>> 
>> Biophys J. 1986 Nov; 50(5): 967–980.
>> doi: 10.1016/S0006-3495(86)83537-8
>> PMCID: PMC1329821
>> PMID: 3790697
>> Water structure in vitamin B12 coenzyme crystals. II. Structural 
>> characteristics of the solvent networks.
>> 
>> H Savage
>> 
>> On Sun, 19 Mar 2023 at 19:37, James Holton  wrote:
>> They say one test is worth a thousand expert opinions, so I tried my hand at 
>> the former.
>> 
>> The question is: what is the right way to treat disordered side chains?:
>> a) omit atoms you cannot see
>> b) build them, and set occupancy to zero
>> c) build them, and "let the B factors take care of it"
>> d) none of the above
>> 
>> The answer, of course, is d).
>> 
>> Oh, c'mon.  Yes, I know one of a,b, or c is what you've been doing your 
>> whole life. I do it too.  But, let's face it: none of these solutions are 
>> perfect.  So, the real question is not which one is "right", but which is 
>> the least wrong?  
>> 
>> We all know what is really going on: the side chain is flapping around. No 
>> doubt it spends most of its time in energetically reasonable but 
>> nevertheless numerous conformations.  There are 41 "Favorable" rotamers for 
>> Lys alone, and it doesn't take that many to spread the density thin enough 
>> to fall below the classical 1-sigma contour level. The atoms are still 
>> there, they are still contributing to the data, and they haven't gone far. 
>> So why don't we "just" model that?  Already, I can hear the cries of 
>> "over-fitting!" and "observations/parameters!", "model bias!", and "think of 
>> the children!"  Believe it or not, none of these are the major issue here. 
>> Allow me to demonstrate:
>> 
>> Consider a simple case where we have a Lys side chain in ten conformers. I 
>> chose from popular rotamers, but evenly spread. That is, all 10 conformers 
>> have an occupancy of 0.10, and there is a 3-3-4 split of chi1 values between 
>> minus, plus and trans.  This will give the maximum contrast of density 
>> between CB and CG.  Let us further require that there is no strain in this 
>> ground-truth. No stretched bonds, no tortured angles, no clashes, etc.  Real 
>> molecules don't occupy such high-energy states unless they absolutely have 
>> to.  Let us further assume that the bulk solvent works the way phenix models 
>> it, which is a probe radius of 1.1 A for both ions and aliphatics and a 
>> shrink radius of 0.9.  But, instead of running one phenix.fmodel job, I ran 
>> ten: one for each conformer (A thru J).  To add some excitement, I moved the 
>> main chain ~0.2 A in a random direction for each conformer. I then took 
>> these ten calculated electron density maps (bulk solvent and all) and added 
>> them together to form the ground truth for the following trials. Before 
>> refinement, I added noise consistent with an I/sigma of 50 and cut the 
>> resolution at 2.0 A. Wilson B is 50:
>> 
>> CCtrue   Rwork%  Rfree%   fo-fc(sigma)   description
>> 0.8943 9.05   10.60  5.9 stump at CB
>> 0.9540 9.29   11.73  6.0 single conformer, zero occupancy
>> 0.947110.35   15.04  5.1 single conformer, full occupancy, 
>> refmac5
>> 0.9523 9.78   15.61  4.9 single conformer, full occupancy, 
>> phenix.refine
>> 
>> So, it would appear that the zero-occupancy choice "wins", but by the 
>> narrowest of margins.  Here CCtrue is the Pearson correlation coefficient 
>> between the ground-truth right-answer electron density and the 2fofc map 
>> resulting from the refinement.  Rwork and Rfree are the usual suspects, and 
>> fo-fc indicates the tallest peak in the difference map. Refinement was with 
>> refmac unless otherwise 

Re: [ccp4bb] To Trim or Not to To Trim

[Harry Powell]

And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or not 
cramin is a protein, since it has “only” 46 amino acids) where (from memory, I 
haven’t read the paper for at least 20 nyears…) they modelled multiple water 
networks.

3NIR, for reference.

Harry


> On 20 Mar 2023, at 10:20, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Thank you for such a careful analysis of modelling a "true" structure. You 
> should publish this James.
> 
> It shows amongst other things, how R factors depend on our modelling of 
> solvent which is not represented as individual atoms (And also I think on how 
> the scales are derived between observation and calculation.)
> Years ago someone refined vitamin B12 against high resolution (0.6A?) data. 
> There is about 20-25% solvent volume I think..t was clear in the maps that 
> there were partially occupied networks of water which extended throughout the 
> lattice. This is probably true for proteins as well, and must affect the 
> conformations of surface sidechains? 
> Eleanor
> The B12creference ...
> 
> Biophys J. 1986 Nov; 50(5): 967–980.
> doi: 10.1016/S0006-3495(86)83537-8
> PMCID: PMC1329821
> PMID: 3790697
> Water structure in vitamin B12 coenzyme crystals. II. Structural 
> characteristics of the solvent networks.
> 
> H Savage
> 
> On Sun, 19 Mar 2023 at 19:37, James Holton  wrote:
> They say one test is worth a thousand expert opinions, so I tried my hand at 
> the former.
> 
> The question is: what is the right way to treat disordered side chains?:
> a) omit atoms you cannot see
> b) build them, and set occupancy to zero
> c) build them, and "let the B factors take care of it"
> d) none of the above
> 
> The answer, of course, is d).
> 
> Oh, c'mon.  Yes, I know one of a,b, or c is what you've been doing your whole 
> life. I do it too.  But, let's face it: none of these solutions are perfect.  
> So, the real question is not which one is "right", but which is the least 
> wrong?  
> 
> We all know what is really going on: the side chain is flapping around. No 
> doubt it spends most of its time in energetically reasonable but nevertheless 
> numerous conformations.  There are 41 "Favorable" rotamers for Lys alone, and 
> it doesn't take that many to spread the density thin enough to fall below the 
> classical 1-sigma contour level. The atoms are still there, they are still 
> contributing to the data, and they haven't gone far. So why don't we "just" 
> model that?  Already, I can hear the cries of "over-fitting!" and 
> "observations/parameters!", "model bias!", and "think of the children!"  
> Believe it or not, none of these are the major issue here. Allow me to 
> demonstrate:
> 
> Consider a simple case where we have a Lys side chain in ten conformers. I 
> chose from popular rotamers, but evenly spread. That is, all 10 conformers 
> have an occupancy of 0.10, and there is a 3-3-4 split of chi1 values between 
> minus, plus and trans.  This will give the maximum contrast of density 
> between CB and CG.  Let us further require that there is no strain in this 
> ground-truth. No stretched bonds, no tortured angles, no clashes, etc.  Real 
> molecules don't occupy such high-energy states unless they absolutely have 
> to.  Let us further assume that the bulk solvent works the way phenix models 
> it, which is a probe radius of 1.1 A for both ions and aliphatics and a 
> shrink radius of 0.9.  But, instead of running one phenix.fmodel job, I ran 
> ten: one for each conformer (A thru J).  To add some excitement, I moved the 
> main chain ~0.2 A in a random direction for each conformer. I then took these 
> ten calculated electron density maps (bulk solvent and all) and added them 
> together to form the ground truth for the following trials. Before 
> refinement, I added noise consistent with an I/sigma of 50 and cut the 
> resolution at 2.0 A. Wilson B is 50:
> 
> CCtrue   Rwork%  Rfree%   fo-fc(sigma)   description
> 0.8943 9.05   10.60  5.9 stump at CB
> 0.9540 9.29   11.73  6.0 single conformer, zero occupancy
> 0.947110.35   15.04  5.1 single conformer, full occupancy, 
> refmac5
> 0.9523 9.78   15.61  4.9 single conformer, full occupancy, 
> phenix.refine
>
> So, it would appear that the zero-occupancy choice "wins", but by the 
> narrowest of margins.  Here CCtrue is the Pearson correlation coefficient 
> between the ground-truth right-answer electron density and the 2fofc map 
> resulting from the refinement.  Rwork and Rfree are the usual suspects, and 
> fo-fc indicates the tallest peak in the difference map. Refinement was with 
> refmac unless otherwise indicated. I think we often forget that both phenix 
> and refmac restrain B factor values, not just through bonds but through 
> space, and they use rather different algorithms. Refmac tries to make the 
> histogram of B factors "look right", whereas phenix allows steeper 

Re: [ccp4bb] To Trim or Not to To Trim

[Eleanor Dodson]

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

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

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

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

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

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

[ccp4bb] Grade Web Server 11th Anniversary and a major upgrade

[Oliver Smart]

Dear all,

The generation of reliable restraints for novel small-molecule ligands in 
macromolecular complexes is of great importance for both ligand placement into 
density maps and subsequent refinement. 

Eleven years ago we announced on the ccp4bb the availability of the Grade Web 
Server (GWS):   

https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;94bd95fa.1203

The GWS is still going strong and can be found at

https://grade.globalphasing.org/

The GWS allowed users to run the Grade ligand restraint generator on any 
non-confidential ligand. The main source of restraint information for Grade is 
the Cambridge Structural Database (CSD) of small-molecule crystal structures, 
queried using the MOGUL program developed by the CCDC. Where small-molecule 
information is lacking, Grade uses computational chemistry procedures to obtain 
the restraint values. As well as CIF restraints (that can be used with Coot, 
Refmac, BUSTER and many other programs), the GWS has the option to produce 
restraints for SHELX refinement. The GWS allows users to produce restraints 
without installing the CSD or other software.

In December the GWS had a major upgrade and now runs Grade2 
https://gphl.gitlab.io/grade2/. The GWS user interface has been simplified. 
Also included is support for a wider range of input and output file formats 
such as SDF. Grade2 has many improvements over Grade, such as better treatment 
of planar groups.

In these first eleven years of service, the GWS has been used to produce 
restraints for over 22,000 ligands. The GWS is used by scientists from across 
the world so far: this year it has been used in 31 different countries. We 
would like to thank users for bug reports, suggestions, discussions, and 
feedback. We are grateful to the CCDC for their continued support of the 
service.

With best wishes,

The Global Phasing developers: Gerard Bricogne, Claus Flensburg, Peter Keller, 
Wlodek Paciorek, Andrew Sharff, Oliver Smart, Clemens Vonrhein, and Thomas 
Womack.


P.S. There is now a wide range of excellent restraint generation programs 
available, as reviewed by Steiner and Tucker, 2017 
(https://doi.org/10.1107/S2059798316017964), including CCP4 ACEDRG and Phenix 
eLBOW.  In most cases, good results can be obtained with all of these but for 
unusual chemistry it is often worth trying another program.


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Re: [ccp4bb] To Trim or Not to To Trim

[Guillaume Gaullier]

Yes, I meant maps from SPA. This is the great thing about cryoEM: most maps are 
discovery maps!

I agree that showing crystallographic maps requires more careful explanations 
for non-experts, but I still believe we, as a field trying to make our nerdy 
technical things more approachable to others, are better off showing maps than 
not.

Cheers,

Guillaume


On 17 Mar 2023, at 23:57, Huw Jenkins 
mailto:h.t.jenk...@me.com>> wrote:



On 17 Mar 2023, at 15:01, Guillaume Gaullier 
mailto:guillaume.gaull...@kemi.uu.se>> wrote:

CryoEM papers often show a map in a main figure, and as a reader I think it is 
very nice to show me the map that convinced you of some finding before showing 
me your interpretation of this map.

Surely a key difference is that cryoEM maps (assuming you mean SPA) are not 
calculated with phases derived from the model shown built into the map?

Most maps shown to convince the reader of the validity of the authors 
interpretation of the electron density in X-ray crystallography papers use some 
attempt at removing bias from 2Fo-Fc or Fo-Fc density when the phases have at 
some point in the refinement been derived from a model including the region of 
interest. Few are “discovery maps” to use Dale Tronrud’s term: 
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg04276.html


Huw

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