[ccp4bb] South American Macromolecular Crystallography School

[Nicole Larrieux]

Dear colleagues,

We are pleased to announce the 8th South American Macromolecular 
Crystallography School 2021 "Structural Biology to enhance high impact research 
in health and disease” to be held from Sep 20 to Oct 1, 2021
Please find the application form and further information at 
http://pasteur.uy/novedades/mx2021/

The application deadline is June 30, 2021. For further inquiries contact 
mx2...@pasteur.edu.uy

Main Topics:
· data collection (remotely @ Diamond synchrotron);
· data processing;
· phasing and structure determination;
· model refinement and validation.

25 participants will be selected, prioritizing advanced PhD students, postdocs 
and young researchers. No registration fee, please look in the www site for 
details on application procedures.
Participants will have the opportunity to collect data from their own crystals 
at Diamond Light Source synchrotron via remote access, with the assistance of 
Diamond staff.
The workshop will be virtual considering the pandemics constraints. It will 
combine excellent lectures with hands-on problem-solving sessions. Tutorials of 
state-of-the-art software will include XDS, Dials, Phaser, ShelX, Coot, Refmac, 
Buster-TNT, PISA, among others.
Since the workshop is virtual additional participants may elect to attend 
lectures only. If you wish to do this please complete the registration form and 
indicate that this is your choice.

Invited speakers and tutors :
• Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil)
• Kevin Cowtan (University of York, UK)
• Eleanor Dodson (University of York, UK)
• Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK)
• Elspeth Garman (University of Oxford, UK)
• Beatriz Guimarāes (Instituto Carlos Chagas Fiocruz, Curitiba, Brazil)
• Marin van Heel (Lab. Nacional de Nanotecnologia CNPEM, Campinas, Brazil)
• Ronan Keegan (STFC Rutherford Appleton Lab – CCP4, Didcot, UK)
• Eugene Krissinel (STFC Rutherford Appleton Lab – CCP4, Didcot, UK)
• Andrey Lebedev (STFC Rutherford Appleton Lab – CCP4, Didcot, UK)
• Natalia Lisa (Instituto de Biología Molecular y Celular, Rosario, Argentina)
• Joāo Muniz (Instituto de Física de São Carlos, Brazil)
• Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK)
• James Parkhurst (Diamond Light Source, Didcot, UK)
• Randy Read (University of Cambridge, UK)
• Silvia Russi (Stanford Synchrotron Radiation Lightsource, USA)
• Nukri Sanishvili (Argonne National Laboratory, Chicago, USA)
• Isabel Usón (Instituto de Biología Molecular de Barcelona, Spain)
• Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK)

Organizers:
Nicole Larrieux, Clinical Biochemist. Institut Pasteur de Montevideo, Uruguay
Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom
Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay


This Workshop is supported by the Collaborative Computational Project Nº4 
(CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de 
Biologia Estructural del Mercosur (CeBEM); and the Programa Iberoamericano de 
Ciencia y Tecnologia para el Desarrollo (CYTED) through de MICROBES consortium.

Looking forward to seeing you at the Workshop!

Nicole, Alejandro, Kyle and Ronan



Nicole Larrieux

Laboratory of Molecular & Structural Microbiology
Institut Pasteur de Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY
Phone: +598 25220910 int. 143
Fax:  +598 25224185
http://pasteur.uy/en/research/labs/molecular-and-structural-microbiology-lab



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Re: [ccp4bb] Analysis of NMR ensembles

[Dale Tronrud]

   You are much more knowledgeable than me about the details of 
structure determination via resonance spectroscopy.  I was attempting to 
come up with a toy example that showed that there are reasons for the 
absence of cross-peaks other than flexibility.  I accept that the 
misinterpretation I proposed would be difficult for a careful 
experimenter to make.


   I do get uncomfortable when I'm told that A implies B in a well 
executed experiment but I have no way of knowing if the model I'm 
looking at was constructed via a "well executed experiment".  Am I right 
that the PDB still has no validation slider for the quality of the fit 
of an NMR model to its data?


   I know, via existence proofs, that there are crystallographic models 
in the PDB that fit their data poorly or are simply unjustified by the 
experimental results.  Does this never happen with NMR?  How can I know 
that the model I'm looking at in the PDB was created using all the 
powerful techniques you describe, and that those techniques were 
correctly performed?


   Only with knowledge of those details can I say that the model I'm 
looking at is one of your "well-determined NMR ensembles" and I can 
trust that the variability in the ensemble reflects the structural 
variability.


Dale Tronrud

On 5/26/2021 2:38 PM, Mark J. van Raaij wrote:

Dear Dale,
Aren’t NMR spectroscopists, in contrast to us crystallographers, not in the 
lucky situation though that they should have noticed the absence of terminal 
residues during the assignment phase though? I.e. they would usually have peaks 
for the protons of those residues in the 1D, TOCSY, COSY spectra, even though 
NOEs may be absent.
I agree with you that other reasons than flexibility could cause absence of 
NOE’s, although I think that for well-determined NMR ensembles in almost all 
cases it is indeed flexibility / multiple conformations. If not enough 
restraints have been input, you might get artificial “flexible” regions, and 
obtaining more NOEs, secondary structure restraints, measuring orientational 
restraints should shore these up.
(Assuming that in the previous assignent phase all protons peaks could be 
properly assigned of course).
Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/



On 26 May 2021, at 23:06, Dale Tronrud  wrote:

Dear Boaz,

   We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) arise 
from their flexibility, ..."  This makes it sound like you agree that these 
deficiencies in other regions may be caused by properties other than flexibility.

   As an extreme example, the N-terminal region of a protein may have a broad 
distribution in the ensemble model either because this region experiences many 
conformations in solution, or because this peptide was cleaved from the protein 
at some earlier time and its absence was not recognized by the experimentalist.

Dale Tronrud

On 5/26/2021 1:06 PM, Boaz Shaanan wrote:

Hi Dale and Cecil,
This is quite a circular argument, isn't it? Deficient NOE's for some regions 
(e.g. loops) arise from their flexibility, hence they are not as well resolved 
as other (e.g. internal ) regions for which the number of NOE is large. So they 
are flexible by all accounts and, not surprisingly, align usually with high 
B-factor regions in the corresponding crystal structures. In cases where such 
flexible regions are held by crystal contacts the situations would likely be 
different.
Cheers,
Boaz
/Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710 /
//
//
/
/

*From:* CCP4 bulletin board  on behalf of Dale Tronrud 

*Sent:* Wednesday, May 26, 2021 10:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] Analysis of NMR ensembles
 I agree with Dr Breyton. The variability in an NMR ensemble does not
reflect "mobility" but simply "uncertainty" in conformation.  The spread
in coordinates in some regions simply reflects the lack of experimental
data which could define a single conformation.  There are many reasons
why these data are be absent and high mobility is only one.
Dale Tronrud
On 5/26/2021 8:45 AM, Cécile Breyton wrote:

Hello,
In my understanding of NMR, the loops and terminii that adopt very different 
conformations in the structure ensemble rather reflect the fact that for those 
residues, the number of constraints is lower, thus the number of structures 
that fulfil the constraints is larger A dynamics study of the protein will 
be much more informative.
Cécile
Le 26/05/2021 à 17:29, S. Mohanty a écrit :

Hi Harry,

The superpose/overlay of all the structures in PyMol should inform you the 
rigid part of the 

Re: [ccp4bb] Analysis of NMR ensembles

[Mark J. van Raaij]

Dear Dale,
Aren’t NMR spectroscopists, in contrast to us crystallographers, not in the 
lucky situation though that they should have noticed the absence of terminal 
residues during the assignment phase though? I.e. they would usually have peaks 
for the protons of those residues in the 1D, TOCSY, COSY spectra, even though 
NOEs may be absent.
I agree with you that other reasons than flexibility could cause absence of 
NOE’s, although I think that for well-determined NMR ensembles in almost all 
cases it is indeed flexibility / multiple conformations. If not enough 
restraints have been input, you might get artificial “flexible” regions, and 
obtaining more NOEs, secondary structure restraints, measuring orientational 
restraints should shore these up.
(Assuming that in the previous assignent phase all protons peaks could be 
properly assigned of course).
Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 26 May 2021, at 23:06, Dale Tronrud  wrote:
> 
> Dear Boaz,
> 
>   We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) 
> arise from their flexibility, ..."  This makes it sound like you agree that 
> these deficiencies in other regions may be caused by properties other than 
> flexibility.
> 
>   As an extreme example, the N-terminal region of a protein may have a broad 
> distribution in the ensemble model either because this region experiences 
> many conformations in solution, or because this peptide was cleaved from the 
> protein at some earlier time and its absence was not recognized by the 
> experimentalist.
> 
> Dale Tronrud
> 
> On 5/26/2021 1:06 PM, Boaz Shaanan wrote:
>> Hi Dale and Cecil,
>> This is quite a circular argument, isn't it? Deficient NOE's for some 
>> regions (e.g. loops) arise from their flexibility, hence they are not as 
>> well resolved as other (e.g. internal ) regions for which the number of NOE 
>> is large. So they are flexible by all accounts and, not surprisingly, align 
>> usually with high B-factor regions in the corresponding crystal structures. 
>> In cases where such flexible regions are held by crystal contacts the 
>> situations would likely be different.
>> Cheers,
>>Boaz
>> /Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben-Gurion University of the Negev
>> Beer-Sheva 84105
>> Israel
>> E-mail: bshaa...@bgu.ac.il
>> Phone: 972-8-647-2220
>> Fax:   972-8-647-2992 or 972-8-646-1710 /
>> //
>> //
>> /
>> /
>> 
>> *From:* CCP4 bulletin board  on behalf of Dale 
>> Tronrud 
>> *Sent:* Wednesday, May 26, 2021 10:46 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK 
>> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles
>> I agree with Dr Breyton. The variability in an NMR ensemble does not
>> reflect "mobility" but simply "uncertainty" in conformation.  The spread
>> in coordinates in some regions simply reflects the lack of experimental
>> data which could define a single conformation.  There are many reasons
>> why these data are be absent and high mobility is only one.
>> Dale Tronrud
>> On 5/26/2021 8:45 AM, Cécile Breyton wrote:
>>> Hello,
>>> In my understanding of NMR, the loops and terminii that adopt very 
>>> different conformations in the structure ensemble rather reflect the fact 
>>> that for those residues, the number of constraints is lower, thus the 
>>> number of structures that fulfil the constraints is larger A dynamics 
>>> study of the protein will be much more informative.
>>> Cécile
>>> Le 26/05/2021 à 17:29, S. Mohanty a écrit :
 Hi Harry,
 
 The superpose/overlay of all the structures in PyMol should inform you the 
 rigid part of the protein as well as the flexible part. The rigid part 
 would have very low backbone RMSD or overlay tightly and the flexible part 
 (loops, N-term and C-term etc.) would not superpose tightly. If you check 
 literature, the dynamics of the protein may have been studied through NMR 
 relaxation.
 
 Smita
 
 
 On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
 <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
 
 
 Hi
 
 Given that there are plenty of people on this BB who are structural 
 biologists rather than “just” crystallographers, I thought someone here 
 might be able to help.
 
 If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
 structures that fit the NOEs, is there a tool available that will give me 
 some idea about the bits of the structure that do not vary much (“rigid”) 
 and the bits that are all over the place (“flexible”)?
 
 Would superpose or gesamt be a good tool for this? Ideally I’d like 
 something that could add a figure to the B columns in a PDB file so I 
 could see 

Re: [ccp4bb] Analysis of NMR ensembles

[Dale Tronrud]

Dear Boaz,

   We are likely in agreement. "Deficient NOE's for some regions (e.g. 
loops) arise from their flexibility, ..."  This makes it sound like you 
agree that these deficiencies in other regions may be caused by 
properties other than flexibility.


   As an extreme example, the N-terminal region of a protein may have a 
broad distribution in the ensemble model either because this region 
experiences many conformations in solution, or because this peptide was 
cleaved from the protein at some earlier time and its absence was not 
recognized by the experimentalist.


Dale Tronrud

On 5/26/2021 1:06 PM, Boaz Shaanan wrote:

Hi Dale and Cecil,

This is quite a circular argument, isn't it? Deficient NOE's for some 
regions (e.g. loops) arise from their flexibility, hence they are not as 
well resolved as other (e.g. internal ) regions for which the number of 
NOE is large. So they are flexible by all accounts and, not 
surprisingly, align usually with high B-factor regions in the 
corresponding crystal structures. In cases where such flexible regions 
are held by crystal contacts the situations would likely be different.


Cheers,

                Boaz


/Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710 /
//
//
/

/

*From:* CCP4 bulletin board  on behalf of Dale 
Tronrud 

*Sent:* Wednesday, May 26, 2021 10:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] Analysis of NMR ensembles
     I agree with Dr Breyton. The variability in an NMR ensemble does not
reflect "mobility" but simply "uncertainty" in conformation.  The spread
in coordinates in some regions simply reflects the lack of experimental
data which could define a single conformation.  There are many reasons
why these data are be absent and high mobility is only one.

Dale Tronrud

On 5/26/2021 8:45 AM, Cécile Breyton wrote:

Hello,

In my understanding of NMR, the loops and terminii that adopt very 
different conformations in the structure ensemble rather reflect the 
fact that for those residues, the number of constraints is lower, thus 
the number of structures that fulfil the constraints is larger A 
dynamics study of the protein will be much more informative.


Cécile

Le 26/05/2021 à 17:29, S. Mohanty a écrit :

Hi Harry,

The superpose/overlay of all the structures in PyMol should inform you 
the rigid part of the protein as well as the flexible part. The rigid 
part would have very low backbone RMSD or overlay tightly and the 
flexible part (loops, N-term and C-term etc.) would not superpose 
tightly. If you check literature, the dynamics of the protein may have 
been studied through NMR relaxation.


Smita


On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:



Hi

Given that there are plenty of people on this BB who are structural 
biologists rather than “just” crystallographers, I thought someone 
here might be able to help.


If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
structures that fit the NOEs, is there a tool available that will give 
me some idea about the bits of the structure that do not vary much 
(“rigid”) and the bits that are all over the place (“flexible”)?


Would superpose or gesamt be a good tool for this? Ideally I’d like 
something that could add a figure to the B columns in a PDB file so I 
could see something in QTMG (or PyMol if forced…) or do other useful 
things with the information.


Harry



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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 


>



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Re: [ccp4bb] Analysis of NMR ensembles

[Boaz Shaanan]

Hi Dale and Cecil,

This is quite a circular argument, isn't it? Deficient NOE's for some regions 
(e.g. loops) arise from their flexibility, hence they are not as well resolved 
as other (e.g. internal ) regions for which the number of NOE is large. So they 
are flexible by all accounts and, not surprisingly, align usually with high 
B-factor regions in the corresponding crystal structures. In cases where such 
flexible regions are held by crystal contacts the situations would likely be 
different.

Cheers,

   Boaz




Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710





From: CCP4 bulletin board  on behalf of Dale Tronrud 

Sent: Wednesday, May 26, 2021 10:46 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Analysis of NMR ensembles

I agree with Dr Breyton. The variability in an NMR ensemble does not
reflect "mobility" but simply "uncertainty" in conformation.  The spread
in coordinates in some regions simply reflects the lack of experimental
data which could define a single conformation.  There are many reasons
why these data are be absent and high mobility is only one.

Dale Tronrud

On 5/26/2021 8:45 AM, Cécile Breyton wrote:
> Hello,
>
> In my understanding of NMR, the loops and terminii that adopt very
> different conformations in the structure ensemble rather reflect the
> fact that for those residues, the number of constraints is lower, thus
> the number of structures that fulfil the constraints is larger A
> dynamics study of the protein will be much more informative.
>
> Cécile
>
> Le 26/05/2021 à 17:29, S. Mohanty a écrit :
>> Hi Harry,
>>
>> The superpose/overlay of all the structures in PyMol should inform you
>> the rigid part of the protein as well as the flexible part. The rigid
>> part would have very low backbone RMSD or overlay tightly and the
>> flexible part (loops, N-term and C-term etc.) would not superpose
>> tightly. If you check literature, the dynamics of the protein may have
>> been studied through NMR relaxation.
>>
>> Smita
>>
>>
>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Hi
>>
>> Given that there are plenty of people on this BB who are structural
>> biologists rather than “just” crystallographers, I thought someone
>> here might be able to help.
>>
>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of
>> structures that fit the NOEs, is there a tool available that will give
>> me some idea about the bits of the structure that do not vary much
>> (“rigid”) and the bits that are all over the place (“flexible”)?
>>
>> Would superpose or gesamt be a good tool for this? Ideally I’d like
>> something that could add a figure to the B columns in a PDB file so I
>> could see something in QTMG (or PyMol if forced…) or do other useful
>> things with the information.
>>
>> Harry
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>>
>>
>> This message was issued to members of 
>> www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms 
>> & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>> 
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>
>
> 
>
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Re: [ccp4bb] Analysis of NMR ensembles

[Dale Tronrud]

   I agree with Dr Breyton. The variability in an NMR ensemble does not 
reflect "mobility" but simply "uncertainty" in conformation.  The spread 
in coordinates in some regions simply reflects the lack of experimental 
data which could define a single conformation.  There are many reasons 
why these data are be absent and high mobility is only one.


Dale Tronrud

On 5/26/2021 8:45 AM, Cécile Breyton wrote:

Hello,

In my understanding of NMR, the loops and terminii that adopt very 
different conformations in the structure ensemble rather reflect the 
fact that for those residues, the number of constraints is lower, thus 
the number of structures that fulfil the constraints is larger A 
dynamics study of the protein will be much more informative.


Cécile

Le 26/05/2021 à 17:29, S. Mohanty a écrit :

Hi Harry,

The superpose/overlay of all the structures in PyMol should inform you 
the rigid part of the protein as well as the flexible part. The rigid 
part would have very low backbone RMSD or overlay tightly and the 
flexible part (loops, N-term and C-term etc.) would not superpose 
tightly. If you check literature, the dynamics of the protein may have 
been studied through NMR relaxation.


Smita


On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:



Hi

Given that there are plenty of people on this BB who are structural 
biologists rather than “just” crystallographers, I thought someone 
here might be able to help.


If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
structures that fit the NOEs, is there a tool available that will give 
me some idea about the bits of the structure that do not vary much 
(“rigid”) and the bits that are all over the place (“flexible”)?


Would superpose or gesamt be a good tool for this? Ideally I’d like 
something that could add a figure to the B columns in a PDB file so I 
could see something in QTMG (or PyMol if forced…) or do other useful 
things with the information.


Harry



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




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Re: [ccp4bb] Analysis of NMR ensembles

[Michal Jamroz]

Dnia 2021-05-26, o godz. 16:04:59
Harry Powell - CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> napisał(a):
> is there a tool available that will
> give me some idea about the bits of the structure that do not vary
> much (“rigid”) and the bits that are all over the place (“flexible”)?

have a look on theseus https://theobald.brandeis.edu/theseus/ - that's
the tool you are looking for.

if you would like to compare structures to those ensembles, you might
be interested in flexscore https://pubmed.ncbi.nlm.nih.gov/27307633/
(autopromotionxD).

have fun!



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Re: [ccp4bb] Analysis of NMR ensembles

[Bernhard Rupp]

https://pubmed.ncbi.nlm.nih.gov/8744573/

Old but worked...

Best br

On Wed, May 26, 2021, 19:43 Tristan Croll  wrote:

> (sending properly this time, rather than just to Rasmus)
>
> I don't believe a "color by RMS" option is in ChimeraX right now (I'll
> suggest it to the developers), but this will align all models then set
> B-factors for each residue to the RMS CA deviation from the mean position.
> Could be extended fairly trivially to do all-atom RMS if you wanted to.
> Change the extension for the attached text file to .py, open your NMR
> ensemble in ChimeraX, select all the models (typically just "sel #1" should
> do the trick), then use File/Open and choose color_by_rms.py (or just "open
> color_by_rms.py" on the command line if it's in your working directory). As
> long as all models have the same set of residues, it should do the trick.
> Example image for 2kv5 attached.
>
> Have fun!
>
> -- Tristan
> --
> *From:* CCP4 bulletin board  on behalf of Harry
> Powell - CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* 26 May 2021 16:04
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] Analysis of NMR ensembles
>
> Hi
>
> Given that there are plenty of people on this BB who are structural
> biologists rather than “just” crystallographers, I thought someone here
> might be able to help.
>
> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of
> structures that fit the NOEs, is there a tool available that will give me
> some idea about the bits of the structure that do not vary much (“rigid”)
> and the bits that are all over the place (“flexible”)?
>
> Would superpose or gesamt be a good tool for this? Ideally I’d like
> something that could add a figure to the B columns in a PDB file so I could
> see something in QTMG (or PyMol if forced…) or do other useful things with
> the information.
>
> Harry
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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> --
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Re: [ccp4bb] Analysis of NMR ensembles

[Tristan Croll]

(sending properly this time, rather than just to Rasmus)

I don't believe a "color by RMS" option is in ChimeraX right now (I'll suggest 
it to the developers), but this will align all models then set B-factors for 
each residue to the RMS CA deviation from the mean position. Could be extended 
fairly trivially to do all-atom RMS if you wanted to. Change the extension for 
the attached text file to .py, open your NMR ensemble in ChimeraX, select all 
the models (typically just "sel #1" should do the trick), then use File/Open 
and choose color_by_rms.py (or just "open color_by_rms.py" on the command line 
if it's in your working directory). As long as all models have the same set of 
residues, it should do the trick. Example image for 2kv5 attached.

Have fun!

-- Tristan

From: CCP4 bulletin board  on behalf of Harry Powell - 
CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: 26 May 2021 16:04
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Analysis of NMR ensembles

Hi

Given that there are plenty of people on this BB who are structural biologists 
rather than “just” crystallographers, I thought someone here might be able to 
help.

If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures 
that fit the NOEs, is there a tool available that will give me some idea about 
the bits of the structure that do not vary much (“rigid”) and the bits that are 
all over the place (“flexible”)?

Would superpose or gesamt be a good tool for this? Ideally I’d like something 
that could add a figure to the B columns in a PDB file so I could see something 
in QTMG (or PyMol if forced…) or do other useful things with the information.

Harry


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from chimerax.atomic import Residues, Atoms, selected_residues
from math import sqrt
import numpy
models = selected_residues(session).unique_structures
from chimerax.core.commands import run

run(session, f'match {"|".join(["#"+m.id_string for m in models[1:]])} to 
#{models[0].id_string}')

for residues in zip(*[m.residues for m in models]):
residues = Residues(residues)
pas = Atoms(residues.principal_atoms)
if not len(pas):
residues.atoms.bfactors = 0
continue

coords = pas.scene_coords
avg = numpy.mean(coords, axis=0)
deviations = coords-avg
distances = numpy.linalg.norm(deviations, axis=0)
rms = sqrt(numpy.mean(distances**2))
residues.atoms.bfactors = rms

run(session, f'color bfactor sel')



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Re: [ccp4bb] Analysis of NMR ensembles

[Rasmus Fogh]

Hi,

It has been a bit since I was in NMR, but I would propose CYRANGE 
(http://www.bpc.uni-frankfurt.de/cyrange.html), based on the 
recommendation of the PDB NMR Validation Task Force 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884077/).


You can do both superposition and per-residue RMSD and find a way of 
exporting the values to a PDB file somehow, in CcpNmr Analysis 
(https://www.ccpn.ac.uk/), but that is a full NMR analysis package (even 
if it is quite user-friendly ;-) ).


All the best,
Rasmus


On 26/05/2021 16:04, Harry Powell - CCP4BB wrote:

Hi

Given that there are plenty of people on this BB who are structural biologists 
rather than “just” crystallographers, I thought someone here might be able to 
help.

If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures 
that fit the NOEs, is there a tool available that will give me some idea about 
the bits of the structure that do not vary much (“rigid”) and the bits that are 
all over the place (“flexible”)?

Would superpose or gesamt be a good tool for this? Ideally I’d like something 
that could add a figure to the B columns in a PDB file so I could see something 
in QTMG (or PyMol if forced…) or do other useful things with the information.

Harry


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--
Rasmus H. Fogh   Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
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Re: [ccp4bb] Analysis of NMR ensembles

[Jon Cooper]

Hello Harry,

Looking at:

http://www.mcgnmr.mcgill.ca/ProtSkin/

It says: "If your input is a plain file containing your scalar data to map, 
such as heteronuclear NOE or chemical shift differences, ensure the first 
column in your file contains residue numbers and the second column contains the 
values to map, then click the Browse button to retrieve this file and select 
"Plain list of scores"

If you can get the residue number and rmsd data into columns in a file, it 
should map them onto a pdb file for one monomer as pseudo-B-factors.

HTH, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 26 May 2021, 16:51, Harry Powell - CCP4BB wrote:

> Yes, Jon, but I was hoping I wasn’t the first person to ever want this…
>
> Harry
>
>> On 26 May 2021, at 16:34, Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> The hard bit is to get the rmsd's into the B-factor column, but it shouldn't 
>> stretch you too much, Harry ;-
>>
>> There is ProtSkin on the web which does something similar with sequence 
>> alignments.
>>
>> Sent from ProtonMail mobile
>>
>>
>>
>>  Original Message 
>> On 26 May 2021, 16:28, Harry Powell - CCP4BB < 
>> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Hi Jurgen
>>
>> NMR structures don’t appear to have B_factors, or at least not meaningful 
>> ones (e.g. in 2kv5 they’re all 0.00…).
>>
>> thanks for the response, though
>>
>> Harry
>>
>> > On 26 May 2021, at 16:21, Jurgen Bosch  wrote:
>> >
>> > How about color by B-factor and look for the cold areas and hot areas?
>> > Jürgen
>> >
>> >> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
>> >> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> >>
>> >> Hi
>> >>
>> >> Given that there are plenty of people on this BB who are structural 
>> >> biologists rather than “just” crystallographers, I thought someone here 
>> >> might be able to help.
>> >>
>> >> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
>> >> structures that fit the NOEs, is there a tool available that will give me 
>> >> some idea about the bits of the structure that do not vary much (“rigid”) 
>> >> and the bits that are all over the place (“flexible”)?
>> >>
>> >> Would superpose or gesamt be a good tool for this? Ideally I’d like 
>> >> something that could add a figure to the B columns in a PDB file so I 
>> >> could see something in QTMG (or PyMol if forced…) or do other useful 
>> >> things with the information.
>> >>
>> >> Harry
>> >> 
>> >>
>> >> To unsubscribe from the CCP4BB list, click the following link:
>> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> >>
>> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a 
>> >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
>> >> available at https://www.jiscmail.ac.uk/policyandsecurity/
>> >
>> > 
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Analysis of NMR ensembles

[Cécile Breyton]

Hello,

In my understanding of NMR, the loops and terminii that adopt very 
different conformations in the structure ensemble rather reflect the 
fact that for those residues, the number of constraints is lower, thus 
the number of structures that fulfil the constraints is larger A 
dynamics study of the protein will be much more informative.


Cécile

Le 26/05/2021 à 17:29, S. Mohanty a écrit :

Hi Harry,

The superpose/overlay of all the structures in PyMol should inform you 
the rigid part of the protein as well as the flexible part. The rigid 
part would have very low backbone RMSD or overlay tightly and the 
flexible part (loops, N-term and C-term etc.) would not superpose 
tightly. If you check literature, the dynamics of the protein may have 
been studied through NMR relaxation.


Smita


On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:



Hi

Given that there are plenty of people on this BB who are structural 
biologists rather than “just” crystallographers, I thought someone 
here might be able to help.


If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
structures that fit the NOEs, is there a tool available that will give 
me some idea about the bits of the structure that do not vary much 
(“rigid”) and the bits that are all over the place (“flexible”)?


Would superpose or gesamt be a good tool for this? Ideally I’d like 
something that could add a figure to the B columns in a PDB file so I 
could see something in QTMG (or PyMol if forced…) or do other useful 
things with the information.


Harry



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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Hi Smita

Yes, that’s the kind of analysis I had in mind.

I have > 700 structures to “look” at so something that would say “these 
residues overlay with a small RMSD so this bit is rigid, but these residues 
don’t, so that part is flexible” ~700 times. 

Using an MG program of any kind would just be a sanity check that I’d use on a 
very few structures (probably no more than ~20-30) to make sure I’m happy with 
the results before automating the whole thing.

Harry

> On 26 May 2021, at 16:29, S. Mohanty  wrote:
> 
> Hi Harry,
> 
> The superpose/overlay of all the structures in PyMol should inform you the 
> rigid part of the protein as well as the flexible part. The rigid part would 
> have very low backbone RMSD or overlay tightly and the flexible part (loops, 
> N-term and C-term etc.) would not superpose tightly. If you check literature, 
> the dynamics of the protein may have been studied through NMR relaxation. 
> 
> Smita
> 
> 
> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 
> Hi
> 
> Given that there are plenty of people on this BB who are structural 
> biologists rather than “just” crystallographers, I thought someone here might 
> be able to help.
> 
> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
> structures that fit the NOEs, is there a tool available that will give me 
> some idea about the bits of the structure that do not vary much (“rigid”) and 
> the bits that are all over the place (“flexible”)?
> 
> Would superpose or gesamt be a good tool for this? Ideally I’d like something 
> that could add a figure to the B columns in a PDB file so I could see 
> something in QTMG (or PyMol if forced…) or do other useful things with the 
> information.
> 
> Harry
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
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Re: [ccp4bb] Analysis of NMR ensembles

[Andrew Raine]

Hi Harry,

(Oooh - after lurking on this list for probably 20 years, I can actually 
comment on something...)



If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of
structures that fit the NOEs, is there a tool available that will
give me some idea about the bits of the structure that do not vary
much (“rigid”) and the bits that are all over the place
(“flexible”)?
I used to use a tool called "uwmn", originally written by Mike Hartshorn 
when he was in York, and extended a bit by myself.


This calculated a "mean interatomic distance matrix" over all the 
structures in an ensemble, for the atoms selected on the command-line 
and then projected it back into 3D (using PCA, or possibly PCoA - I 
can't remember which) to make an "unweighted mean" structure.


It then looped over all the individual structures to calculate a 
least-squares fit to the mean structure, and populated the B-factor 
field with each atom's deviation from the "mean" coordinate.


To solve your problem, I would have first run it on the CA's of the 
whole chain, and looked at the "B-factors" to see where the variability 
was greatest, then iteratively excluded/included bits of backbone until 
I thought I had a structurally-legitimate selection for the 
not-so-variable regions.  Convincing novices to check the ensemble 
visually was an important part of this, I recall.


I'd love to recommend you use Mike's/my code, but I'm not sure whether I 
can find a copy, nor whether it will compile on a modern Linux.  I'll 
try to dig it out...


Best regards,

Andrew

--
Dr. Andrew Raine, Head of IT, MRC Mitochondrial Biology Unit,
Keith Peters Building, Biomedical Campus, Cambridge, CB2 0XY, UK
phone: +44 (0)1223 252830web: www.mrc-mbu.cam.ac.uk
email: a...@mrc-mbu.cam.ac.uk



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Re: [ccp4bb] Analysis of NMR ensembles

[Jurgen Bosch]

I vaguely recall that using MUSTANG you will get the distance between residues 
reflected in the b-value column and then you can color by B-value.

https://lcb.infotech.monash.edu/mustang/mustang_psfb-final.pdf 


Jürgen 

> On May 26, 2021, at 11:28 AM, Harry Powell - CCP4BB 
>  wrote:
> 
> Hi Jurgen
> 
> NMR structures don’t appear to have B_factors, or at least not meaningful 
> ones (e.g. in 2kv5 they’re all 0.00…). 
> 
> thanks for the response, though
> 
> Harry
> 
>> On 26 May 2021, at 16:21, Jurgen Bosch  wrote:
>> 
>> How about color by B-factor and look for the cold areas and hot areas?
>> Jürgen 
>> 
>>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
>>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> Hi
>>> 
>>> Given that there are plenty of people on this BB who are structural 
>>> biologists rather than “just” crystallographers, I thought someone here 
>>> might be able to help.
>>> 
>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
>>> structures that fit the NOEs, is there a tool available that will give me 
>>> some idea about the bits of the structure that do not vary much (“rigid”) 
>>> and the bits that are all over the place (“flexible”)?
>>> 
>>> Would superpose or gesamt be a good tool for this? Ideally I’d like 
>>> something that could add a figure to the B columns in a PDB file so I could 
>>> see something in QTMG (or PyMol if forced…) or do other useful things with 
>>> the information.
>>> 
>>> Harry
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>> 
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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>> 
>> 
>> 
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Re: [ccp4bb] Analysis of NMR ensembles

[Jon Cooper]

The hard bit is to get the rmsd's into the B-factor column, but it shouldn't 
stretch you too much, Harry ;-

There is ProtSkin on the web which does something similar with sequence 
alignments.

Sent from ProtonMail mobile

 Original Message 
On 26 May 2021, 16:28, Harry Powell - CCP4BB wrote:

> Hi Jurgen
>
> NMR structures don’t appear to have B_factors, or at least not meaningful 
> ones (e.g. in 2kv5 they’re all 0.00…).
>
> thanks for the response, though
>
> Harry
>
>> On 26 May 2021, at 16:21, Jurgen Bosch  wrote:
>>
>> How about color by B-factor and look for the cold areas and hot areas?
>> Jürgen
>>
>>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
>>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>
>>> Hi
>>>
>>> Given that there are plenty of people on this BB who are structural 
>>> biologists rather than “just” crystallographers, I thought someone here 
>>> might be able to help.
>>>
>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
>>> structures that fit the NOEs, is there a tool available that will give me 
>>> some idea about the bits of the structure that do not vary much (“rigid”) 
>>> and the bits that are all over the place (“flexible”)?
>>>
>>> Would superpose or gesamt be a good tool for this? Ideally I’d like 
>>> something that could add a figure to the B columns in a PDB file so I could 
>>> see something in QTMG (or PyMol if forced…) or do other useful things with 
>>> the information.
>>>
>>> Harry
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>>> https://www.jiscmail.ac.uk/policyandsecurity/
>>
>> 
>>
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Re: [ccp4bb] Analysis of NMR ensembles

[S. Mohanty]

Hi Harry,
The superpose/overlay of all the structures in PyMol should inform you the 
rigid part of the protein as well as the flexible part. The rigid part would 
have very low backbone RMSD or overlay tightly and the flexible part (loops, 
N-term and C-term etc.) would not superpose tightly. If you check literature, 
the dynamics of the protein may have been studied through NMR relaxation. 
Smita 

On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:  
 
 Hi

Given that there are plenty of people on this BB who are structural biologists 
rather than “just” crystallographers, I thought someone here might be able to 
help.

If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures 
that fit the NOEs, is there a tool available that will give me some idea about 
the bits of the structure that do not vary much (“rigid”) and the bits that are 
all over the place (“flexible”)?

Would superpose or gesamt be a good tool for this? Ideally I’d like something 
that could add a figure to the B columns in a PDB file so I could see something 
in QTMG (or PyMol if forced…) or do other useful things with the information.

Harry


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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Hi Jurgen

NMR structures don’t appear to have B_factors, or at least not meaningful ones 
(e.g. in 2kv5 they’re all 0.00…). 

thanks for the response, though

Harry

> On 26 May 2021, at 16:21, Jurgen Bosch  wrote:
> 
> How about color by B-factor and look for the cold areas and hot areas?
> Jürgen 
> 
>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi
>> 
>> Given that there are plenty of people on this BB who are structural 
>> biologists rather than “just” crystallographers, I thought someone here 
>> might be able to help.
>> 
>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
>> structures that fit the NOEs, is there a tool available that will give me 
>> some idea about the bits of the structure that do not vary much (“rigid”) 
>> and the bits that are all over the place (“flexible”)?
>> 
>> Would superpose or gesamt be a good tool for this? Ideally I’d like 
>> something that could add a figure to the B columns in a PDB file so I could 
>> see something in QTMG (or PyMol if forced…) or do other useful things with 
>> the information.
>> 
>> Harry
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>> https://www.jiscmail.ac.uk/policyandsecurity/
> 
> 
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[ccp4bb] Fully-funded PhD at the University of Liverpool

[Rigden, Dan]

Please pass on this information to any plausible candidates you know. Thanks



Title: Efficient matching of protein structures to cryo-EM map segments

Initial deadline: June 30th

This project will develop creative methods and software to efficiently match 
protein structures to cryo-EM map segments. The structures may be complexes, 
chains or domains and may derive from experimental or computational studies. 
The map segments may be derived with reference to map symmetry, by their 
inferred secondary structure composition1 or using signals of supersecondary 
motifs that they contain. The resulting software will eventually be distributed 
as part of the CCP-EM suite.

You will be based in Liverpool but will benefit from extensive collaboration 
with the CCP-EM consortium. You will join a nurturing and productive group with 
a strong track record in software development at the interface between 
bioinformatics and structural biology. You will learn transferable skills in 
computational science and programming, working in an area of biology relevant 
to drug discovery and current health challenges.

Requirements: You will have at least a good B.Sc. 2:1 in Biological or Life 
Sciences, or possibly in a computational subject. An interest in programming, 
especially with Python, is a requirement.

Informal enquiries: drig...@liv.ac.uk.

To apply: please send a CV and covering letter (plus references if available) 
to drig...@liv.ac.uk

Funding: This studentship is funded jointly by CCP-EM and the University of 
Liverpool for 4 years. Funding covers tuition fees at the UK rate only, a 
Research Training and Support Grant (RTSG) and stipend at the UKRI rate 
(currently around £15,600 per year). Funds for travel and conference attendance 
are also included.





Prof Daniel Rigden  (He/Him)
Department of Biochemistry and Systems Biology
Institute of Systems, Molecular and Integrative Biology
Room 101, Biosciences Building
University of Liverpool
Crown St., Liverpool, L69 7ZB

(+44) 151 795 4467
www.liverpool.ac.uk/integrative-biology/staff/daniel-rigden/




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Re: [ccp4bb] Analysis of NMR ensembles

[Jurgen Bosch]

How about color by B-factor and look for the cold areas and hot areas?
Jürgen 

> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi
> 
> Given that there are plenty of people on this BB who are structural 
> biologists rather than “just” crystallographers, I thought someone here might 
> be able to help.
> 
> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of 
> structures that fit the NOEs, is there a tool available that will give me 
> some idea about the bits of the structure that do not vary much (“rigid”) and 
> the bits that are all over the place (“flexible”)?
> 
> Would superpose or gesamt be a good tool for this? Ideally I’d like something 
> that could add a figure to the B columns in a PDB file so I could see 
> something in QTMG (or PyMol if forced…) or do other useful things with the 
> information.
> 
> Harry
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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[ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

Hi

Given that there are plenty of people on this BB who are structural biologists 
rather than “just” crystallographers, I thought someone here might be able to 
help.

If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures 
that fit the NOEs, is there a tool available that will give me some idea about 
the bits of the structure that do not vary much (“rigid”) and the bits that are 
all over the place (“flexible”)?

Would superpose or gesamt be a good tool for this? Ideally I’d like something 
that could add a figure to the B columns in a PDB file so I could see something 
in QTMG (or PyMol if forced…) or do other useful things with the information.

Harry


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Re: [ccp4bb] Unmodeled density

[Fischmann, Thierry]

Public

If the large “blob” sits on a 2-fold crystallographic axis then its occupancy 
is ½.

So one possible interpretation is:

  *   A cation present on the 2-fold axis, occupancy 0.5
  *   Waters next to the cation position, also with occupancy 0.5, even if they 
are not on the 2-fold: the water network / cation alternate in the lattice.

Thierry

On 26 May 2021, at 15:20, leo john 
mailto:ljohn16012...@gmail.com>> wrote:

Hi All:

Thank You very much for the response and yes it is at symmetry axis. Distance 
between the bigger blob and smaller ones is approx 1.45 Ang.
I have tried fitting BO3, BO4, but no luck?

Thanks
John

On Wed, May 26, 2021 at 2:14 PM Pearce, N.M. (Nick) 
mailto:n.m.pea...@uu.nl>> wrote:
Is it on a symmetry axis? If so it could be the superposition of two molecules 
(a molecule and a copy of itself).


On 26 May 2021, at 15:08, leo john 
mailto:ljohn16012...@gmail.com>> wrote:

Hi Group
Can you please suggest what this unmodeled blob can be (see appended picture)?
I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked 
in GOL.

I have tried fitting PO4 and SO4 so far.

Thank You
John




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Re: [ccp4bb] Unmodeled density

[Mark J. van Raaij]

oh, 1.45 Å is a very short distance for metal coordination.
perchlorate has a Cl to O distance of that length
https://en.wikipedia.org/wiki/Perchlorate

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 26 May 2021, at 15:20, leo john  wrote:
> 
> Hi All:
> 
> Thank You very much for the response and yes it is at symmetry axis. Distance 
> between the bigger blob and smaller ones is approx 1.45 Ang.
> I have tried fitting BO3, BO4, but no luck?
> 
> Thanks 
> John
> 
> On Wed, May 26, 2021 at 2:14 PM Pearce, N.M. (Nick)  > wrote:
> Is it on a symmetry axis? If so it could be the superposition of two 
> molecules (a molecule and a copy of itself). 
> 
>> On 26 May 2021, at 15:08, leo john > > wrote:
>> 
>> Hi Group
>> Can you please suggest what this unmodeled blob can be (see appended 
>> picture)?
>> I have Malonate, Boric Acid and Peg in my condition, and crystals were 
>> soaked in GOL.
>> 
>> I have tried fitting PO4 and SO4 so far.
>> 
>> Thank You
>> John
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
>> 
> 
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Re: [ccp4bb] External: Re: [ccp4bb] Unmodeled density

[Michel Fodje]

That looks like a magnessium hexahydrate.

From: CCP4 bulletin board  On Behalf Of Pearce, N.M. 
(Nick)
Sent: May 26, 2021 7:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: Re: [ccp4bb] Unmodeled density

Is it on a symmetry axis? If so it could be the superposition of two molecules 
(a molecule and a copy of itself).


On 26 May 2021, at 15:08, leo john 
mailto:ljohn16012...@gmail.com>> wrote:

Hi Group
Can you please suggest what this unmodeled blob can be (see appended picture)?
I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked 
in GOL.

I have tried fitting PO4 and SO4 so far.

Thank You
John




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Re: [ccp4bb] Unmodeled density

[Mark J. van Raaij]

PS I’d model a metal and 4 waters and then measure the distances after 
refinement. And then look at M Harding's ActaD papers and try to work out which 
coordination configuration and distances work best. And, when you get the 
chance, run an emission spectrum at the beamline to help identify the putative 
heavy(ish) atom that was co-crystallised.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 26 May 2021, at 15:08, leo john  wrote:
> 
> Hi Group
> Can you please suggest what this unmodeled blob can be (see appended picture)?
> I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked 
> in GOL.
> 
> I have tried fitting PO4 and SO4 so far.
> 
> Thank You
> John
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] Unmodeled density

[Mark J. van Raaij]

the central blob looks too big for B or even for P or S.
Perhaps Zn, Cd? (although you didn’t add it, it might have been in the protein 
buffer or dragged through the purification by the protein?)

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 26 May 2021, at 15:08, leo john  wrote:
> 
> Hi Group
> Can you please suggest what this unmodeled blob can be (see appended picture)?
> I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked 
> in GOL.
> 
> I have tried fitting PO4 and SO4 so far.
> 
> Thank You
> John
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] Unmodeled density

[Sandra Eltschkner]

How about [B(OH)
4]−


From: CCP4 bulletin board  on behalf of Dale Tronrud 

Sent: Wednesday, May 26, 2021 3:21 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Unmodeled density

Something to give context and scale would be helpful.  Two views
would also be good.

Dale Tronrud

On 5/26/2021 6:08 AM, leo john wrote:
> Hi Group
> Can you please suggest what this unmodeled blob can be (see appended
> picture)?
> I have Malonate, Boric Acid and Peg in my condition, and crystals were
> soaked in GOL.
>
> I have tried fitting PO4 and SO4 so far.
>
> Thank You
> John
> image.png
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Unmodeled density

[Dale Tronrud]

   Something to give context and scale would be helpful.  Two views 
would also be good.


Dale Tronrud

On 5/26/2021 6:08 AM, leo john wrote:

Hi Group
Can you please suggest what this unmodeled blob can be (see appended 
picture)?
I have Malonate, Boric Acid and Peg in my condition, and crystals were 
soaked in GOL.


I have tried fitting PO4 and SO4 so far.

Thank You
John
image.png





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Re: [ccp4bb] Unmodeled density

[leo john]

Hi All:

Thank You very much for the response and yes it is at symmetry axis.
Distance between the bigger blob and smaller ones is approx 1.45 Ang.
I have tried fitting BO3, BO4, but no luck?

Thanks
John

On Wed, May 26, 2021 at 2:14 PM Pearce, N.M. (Nick) 
wrote:

> Is it on a symmetry axis? If so it could be the superposition of two
> molecules (a molecule and a copy of itself).
>
> On 26 May 2021, at 15:08, leo john  wrote:
>
> Hi Group
> Can you please suggest what this unmodeled blob can be (see appended
> picture)?
> I have Malonate, Boric Acid and Peg in my condition, and crystals were
> soaked in GOL.
>
> I have tried fitting PO4 and SO4 so far.
>
> Thank You
> John
> 
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>



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Re: [ccp4bb] Unmodeled density

[Pearce, N.M. (Nick)]

Is it on a symmetry axis? If so it could be the superposition of two molecules 
(a molecule and a copy of itself).

On 26 May 2021, at 15:08, leo john 
mailto:ljohn16012...@gmail.com>> wrote:

Hi Group
Can you please suggest what this unmodeled blob can be (see appended picture)?
I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked 
in GOL.

I have tried fitting PO4 and SO4 so far.

Thank You
John






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[ccp4bb] Fwd: Abstract submission deadline extended to 2 June - PSB Symposium "Frontiers in Bioimaging", 1-2 July 2021

[Daouda Traore]

Dear all,

Please note that the abstract submission deadline for the PSB Symposium 
"Frontiers in Bioimaging" (1-2 July 2021) has been extended to 
*Wednesday 2 June*.


For further information: 
https://www.esrf.fr/home/events/conferences/2021/psb-symposium-frontiers-in-bioimaging/call-for-abstracts-for-poster-and-oral-contributions.html 



Best regards,

Florent

On 2021-04-22 17:28, Florent Bernaudat wrote:

   Dear all,

   The Partnership for Structural Biology (PSB), an alliance of
   research institutes (EMBL, ESRF, IBS and ILL) located in Grenoble,
   France, is pleased to announce that the PSB Symposium "Frontiers in
   Bioimaging" will take place on 1-2 July 2021. The meeting will be
   held remotely on a virtual event platform over two afternoons, and
   will include a series of invited and selected talks, interactive
   virtual posters, and interactive virtual lounges.

   This is to announce that registration is now opened (*It's FREE.*
   *Deadline on 27 June 2021*) and the programme is available.

   All participants are invited to submit an abstract for a poster
   and/or an oral presentation (short talks of 10 minutes). *Submission
   deadline on 2 June 2021*. The number of posters is limited to *50*,
   and best poster prizes (*150 euros each*) will be awarded.

   For further information and to check out the exciting collection of
   invited speakers: https://www.esrf.fr/psbsymposium2021
   

   The aim and scope of this meeting is to highlight progress in 3D
   imaging research that bridges the gap between the atomic and
   cellular scales, with spatial resolutions spanning from subnanometer
   to submicrometer range. Featured topics will include: cryo-electron
   tomography, X-ray tomography, volume electron microscopy, image
   analysis, super-resolution microscopy, and correlative approaches.
   The applications of the above methods to address essential questions
   in life sciences is of particular interest.

   Best regards,

   On behalf of the organising committee

   -- 


   Florent Bernaudat, PhD
   PSB Scientific Coordinator/Animator

   Partnership for Structural Biology
   Carl-Ivar Brändén Building- office 018
   71, Avenue des Martyrs,
   CS 90181
   38042 Grenoble cedex 9
   France

   http://www.psb-grenoble.eu  
   Phone: 33 (0) 476 20 94 08
   Fax: 33 (0) 476 20 94 00




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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

[Mooers, Blaine H.M. (HSC)]

If you have PyMOL installed, you can paste the bash function below into your 
.bashrc file, enter 'source .bashrc', and then enter 'bu PDB-ID'.
All that you have to remember a month from now is 'bu'. 

Otherwise, you can replace the pymol command with one of the other commands 
that have been suggested and replace the filename stem with $1.


bu()
{
echo "Write out the biological unit for a PDB file from PyMOL."
if [ $# -lt 1 ]; then
  echo 1>&2 "$0: not enough arguments"
  echo "Supply the PDB-ID."
  echo "Example: bu 3nd4"
  return 2
elif [ $# -gt 1 ]; then
  echo 1>&2 "$0: too many arguments"
  echo "Supply the PDB-ID."
  echo "Example: bu 3nd4"
fi
pymol -c -d "fetch $1,type=pdb1;set all_states,on;save $1bu.pdb,state=0"
}


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Marcin Wojdyr 
[woj...@gmail.com]
Sent: Wednesday, May 26, 2021 2:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] writing coordinates of full biomol into one 
(PDB) file

another one:

gemmi convert --assembly=N input.pdb output.pdb


On Wed, 26 May 2021 at 07:30, Frank von Delft
 wrote:
>
> Thanks for the quick responses!  I was looking for a command-line tool
> (should have said).  Here's the list:
>
> 1. phenix.pdb.biomt_reconstruction
> 2. 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__Makemultimer.py=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=wMMX-ub8O19NLtJDQdelGfFOni2RMO7EVgZG1XZ1Uu4=
>  : 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__watcut.uwaterloo.ca_tools_makemultimer_docs=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=XQ41GNcbJlsckrDR76D9n7YD0eKVop24nJpUYi5pTPA=
>   >
> 3. Quat in pymol: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit_Quat=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=K4dJU4Mq8Mi4SgQB6UFnQcTzfnkCfius8_QsRmWs_ZQ=
>   >
> 4. BiologicalUnit in pymol:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=yOPGY2fznON_wKdKHEXsGbfEj9dij-0NHHTuqHdH6tM=
>   >
>
> (CCP4bb is amazing)
>
> Frank
>
> On 25/05/2021 20:44, Frank von Delft wrote:
> > Hello all - this presumably has a really simple solution:
> >
> > For a PDB file with a (correct) biomolecular assembly record (REMARK
> > 350), what program do I use to generate and write out the coordinates
> > of the biomolecular assembly (or one of them).
> >
> > Thanks
> > Frank
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwIBaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8=Zc5y9vtC54wj1EQkTlPSy1gDJXFDHGKDWtpCUt0pGWs=
> >
> > This message was issued to members of 
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> >  , terms & conditions are
> > available at 
> 

[ccp4bb] PhD position, University of Konstanz

[Olga Mayans]

*PhD Position: molecular structural biology of muscle signalling*

We have a vacancy for a PhD student to join our laboratory at the Department of 
Biology, University of Konstanz, Germany.

Our laboratory studies the molecular mechanisms underpinning the architecture, 
stress response, adaptation and disease process of striated muscle. The focus 
of this PhD project will be on understanding the assembly and regulation of 
biomedically relevant, titin-based signalling nodes in the sarcomere. We apply 
an integrative approach to structural biology that combines a rich variety of 
biochemical, biophysical and structural methodologies (with emphasis on X-ray 
crystallography).

Qualifications

Applicants should hold (or be in the process of acquiring) a Master's degree in 
biochemistry, biophysics, life sciences or related discipline, and be 
interested in learning both laboratory-based and computational analyses as 
applicable to the study of molecular systems. A strong motivation to understand 
and discover the molecular mechanisms that enable function in living cells is 
required. Basic experience in molecular biology and/or recombinant protein 
production is expected. Good command of written and spoken English, the ability 
to work in a team, and good communication and organizational skills are 
required. Some initial knowledge of a structural/biophysical method would be of 
advantage.

Application

Applications should contain the following documents in PDF format:

1. Applicant's CV
2. Copies of original degree transcripts displaying marks obtained
2. *Short* statement of motivation for pursuing PhD studies in molecular 
sciences
3. Contact details of two referees

Informal enquiries and application materials should be submitted by email to:

olga.may...@uni-konstanz.de

The position is now available and applications will be considered until the 
position is filled.

===
Prof. Olga Mayans
Biophysics and Structural Biology
Dept of Biology
University of Konstanz
D-78457 Konstanz,
Germany
Tel: +49 7531 88-2212
olga.may...@uni-konstanz.de
===



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Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

[Marcin Wojdyr]

another one:

gemmi convert --assembly=N input.pdb output.pdb


On Wed, 26 May 2021 at 07:30, Frank von Delft
 wrote:
>
> Thanks for the quick responses!  I was looking for a command-line tool
> (should have said).  Here's the list:
>
> 1. phenix.pdb.biomt_reconstruction
> 2. Makemultimer.py: http://watcut.uwaterloo.ca/tools/makemultimer/docs
> 
> 3. Quat in pymol: https://pymolwiki.org/index.php/BiologicalUnit/Quat
> 
> 4. BiologicalUnit in pymol:
> https://pymolwiki.org/index.php/BiologicalUnit
> 
>
> (CCP4bb is amazing)
>
> Frank
>
> On 25/05/2021 20:44, Frank von Delft wrote:
> > Hello all - this presumably has a really simple solution:
> >
> > For a PDB file with a (correct) biomolecular assembly record (REMARK
> > 350), what program do I use to generate and write out the coordinates
> > of the biomolecular assembly (or one of them).
> >
> > Thanks
> > Frank
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> > available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> 
>
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>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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