[ccp4bb] NIH+DOE request for information for advancing high resolution bioimaging technologies

[Hunter, Mark Steven]

The LCLS at SLAC National Accelerator 
Laboratory is reaching out to the biological 
research community in the context of an NIH-DOE request for 
information (RFI) 
on “strategies to advance the utility of high resolution bioimaging 
technologies that already exist and that need to be created.”

Current instruments at LCLS provide unique capabilities for characterizing 
biological samples at high spatial and temporal resolution allowing key insight 
into structural features or to reveal macromolecular dynamics and energy 
landscapes at ambient temperatures. We wish to address how to further your 
research using the unique capabilities offered by LCLS.

In the context of the RFI, we would appreciate answers to a few specific 
questions:


  *   What biological research in your area of expertise could be advanced with 
LCLS and could drive priorities for new Capabilities?



  *   What are the current gaps and/or challenges with LCLS instruments that 
limit their impact on your research or on the broader area of bioscience?



  *What scientific, methodological, engineering or operational barriers 
limit the use of LCLS by your team or your community?

or we encourage you to directly respond to the RFI 
itself.

Independently of the RFI, we would like to hear your suggestions, both to 
inform immediate term actions such as for the current call for coronavirus 
beamtime, 
and to inform priorities for longer term developments and targeted access to 
LCLS.

We will be happy to discuss this in detail with you or answer any questions 
related to this RFI and LCLS capabilities. Please contact Mark Hunter 
(mhunt...@slac.stanford.edu). We look 
forward to having an active discussion with you about how your research can be 
enabled by LCLS.




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[ccp4bb] Call for submissions of interest in coronavirus research using LCLS

[Hunter, Mark Steven]

Call for submissions of interest in coronavirus research using LCLS
Deadline: 11 May 2020

As part of the Department of Energy Basic Energy Sciences support of research 
into the COVID-19 pandemic, the Linac Coherent Light Source (LCLS) offers 
opportunities to study the structure and dynamics of biological molecules under 
near physiological conditions. More broadly, the X-ray instruments of the LCLS 
facility can be used to address biology, chemistry and materials science 
questions associated with the novel coronavirus, COVID-19, and related 
solutions.

The LCLS facility will provide priority expedited access to researchers working 
on these problems. Experiments are anticipated to commence in the summer, with 
exact timing dependent on the impact of necessary health and safety 
restrictions.

Please complete this brief form 
(https://stanforduniversity.qualtrics.com/jfe/form/SV_86BZDt2QtQFQzjf)
to indicate your interest in access to LCLS for Coronavirus/COVID-19 research. 
We would appreciate a response as soon as possible, and no later than 11 May 
2020 in order for your interests to be factored into our beamtime planning.  
Upon receipt of your form we will contact you to discuss detailed requirements.

A formal call for proposals will be issued when the date for restarting LCLS 
operations has been decided. Proposals will be reviewed on an ongoing basis as 
they are received, and accepted proposals will be scheduled as early as 
feasible.

LCLS will make biolab space available for sample preparation and 
characterization, as needed. Full support for remote access to experiments will 
be arranged where feasible, for those researchers unable to travel to the 
facility. Coordination with experiments using 
SSRL and the SLAC/Stanford 
Cryo-EM facilities is welcome.

Please contact Mark Hunter 
(mhunt...@slac.stanford.edu) for additional 
information and guidance.

For more general information about LCLS, please visit: 
http://lcls.slac.stanford.edu





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[ccp4bb] Test the new sequence and ligand components at PDBe

[John Berrisford]

Dear CCP4BB

 

We are delighted to offer two new components available for beta testing on
our PDBe entry pages: the ProtVista sequence component on the PDBe
macromolecules pages and the LigEnv component on the ligands and
environments pages.

 

The ProtVista sequence view component has replaced our previous sequence
viewer on the PDBe macromolecules pages to help users interactively view
sequence-related data alongside topology and 3D structure. This allows the
display of much more data than was possible through our previous sequence
viewer. Try the ProtVista component on our macromolecules page at

https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/3bow/protein/3.

 

The LigEnv component is a new, interactive component displaying views of
ligand binding sites and will replace the static LigPlot image on our
ligands and environments pages. The viewer displays atomic-level
interactions between ligands and macromolecular binding sites and interacts
with an adjacent Mol* 3D viewer, allowing you to easily highlight key
binding residues in the 3D structure. Try the new LigEnv component on our
ligands and environments page at

https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/4ph9/bound/IBP

 

Links to provide feedback are available in the green section at the bottom
of each page. 

 

Kind Regards,

 

John

 

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




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Re: [ccp4bb] supperpose "to the middle"?

[Eleanor Dodson]

well yes - essentially you first superimpose lobe 1a to lobe1b , then lobe
2a to the superimposed copy lob2b-superposed. The theta  phi  *chi or
omega *angle for the second superstition tells you how rotation there is
between the open and closed form.
There are various ways to do this - lsqkab in CCP4I - GESAMT in CCP4I2 (but
not sure how easy it is to select a lobe..)
Probably possible in COOT but the log file isnt very helpful..
More detailed advice if needed..
Eleanor

On Mon, 27 Apr 2020 at 11:21, vincent Chaptal 
wrote:

> Hi all,
>
> suppose I have a protein made out of 2 lobes that have open and closed
> conformations.
> It is currently possible to supperpose the structure on one lobe and
> visualize the movements undergone by the other lobe. But is there a way to
> visualize this movement "from the middle", where I can see the 2 lobes
> moving to the meeting point instead of just one half moving?
>
> Something like:  /\  ->  II  (instead of //)
>
> Thank you
> Best
> Vincent
> --
>
> Vincent Chaptal, PhD
>
> MMSB -UMR5086
>
> Drug Resistance and Membrane Proteins Laboratory
>
> 7 passage du Vercors
>
> 69007 LYON
>
> FRANCE
>
> +33 4 37 65 29 01
>
> http://mmsb.cnrs.fr/en/
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] supperpose "to the middle"?

[vincent Chaptal]

Hi all,

suppose I have a protein made out of 2 lobes that have open and closed 
conformations.
It is currently possible to supperpose the structure on one lobe and 
visualize the movements undergone by the other lobe. But is there a way 
to visualize this movement "from the middle", where I can see the 2 
lobes moving to the meeting point instead of just one half moving?


Something like:  /\  ->  II  (instead of //)

Thank you
Best
Vincent
--

Vincent Chaptal, PhD

MMSB -UMR5086

Drug Resistance and Membrane Proteins Laboratory

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://mmsb.cnrs.fr/en/





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Re: [ccp4bb] CCP4 7.1 problems

[Fan Jiang]

I met a similar problem when I ran the "Geometry analysis" in coot-0.9. Coot 
crashed with the following words. I had to roll back to ccp4-7.0. My system is 
CentOS 7.

make_df_restraints_indices() 508
---
terminate called after throwing an instance of 'std::length_error'
  what():  vector::_M_default_append
/usr/local/ccp4-7.1/bin/coot: line 333: 34362 Aborted (core 
dumped) $coot_bin "$@"
;;; note: source file /usr/local/ccp4-7.1/share/guile/1.8/ice-9/boot-9.scm
;;;   newer than compiled /usr/lib64/guile/2.0/ccache/ice-9/boot-9.go
Throw without catch before boot:
Throw to key syntax-error with args ("memoization" "In file ~S, line ~S: ~A 
~S." ("/usr/local/ccp4-7.1/share/guile/1.8/ice-9/boot-9.scm" 101 "Bad define 
placement" (define (toplevel-env? env) (or (not (pair? env)) (not (pair? (car 
env)) #f)Aborting.
/usr/local/ccp4-7.1/bin/coot: line 333: 41050 Aborted (core 
dumped) guile --version
failed to launch the crash catcher



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[ccp4bb] summary of replies, superimposition of 3D structures using the dsDNA part only

[Fred Vellieux]

Dear all,

I obtained the following suggestions to my query on the BB 
(superimposing two protein:dsDNA structures using the dsDNA structures 
alone for the superposition operation):


- Matthias Barone (fmp-berlin) suggested Chimera, with some instructions 
on "how to do it". He also suggested a program called moloc;


- Anat Bashan (Weizmann) suggested Coot, Calculate, LSQ Superimpose;

- Tim Gruene (univie) suggested Uppsala software factory's lsqman;

- Paul Emsley (MRC-LMB) mentioned that there was no "gesamt" for DNA 
(too bad) and further suggested lsq-improve;


- Jeremy (Tame ?, jt...@yokohama-cu.ac.jp) mentioned a program in c 
called cfit, which he can provide on request.


In the end I used Chimera using the instructions given by Matthias 
Barone and that worked like a charm. So to speak: the result obtained 
was what I wished to find out.


Thanks to all who replied. Superposition using the nucleid acid part of 
complexes can be very informative.


Have a nice day further,

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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

[Harry Powell - CCP4BB]

Hi folks

I can’t help feeling that if there are data extending to 0.97Å and there are 
multiple conformations/multiple components occupying the same region of (real) 
space/non-unity occupancies, the problem is crying out for SHELXL…

Harry

> On 27 Apr 2020, at 07:53, Schreuder, Herman /DE  
> wrote:
> 
> Dear Abhishek,
> 
> I did not follow the links given by Paul. However the way I proceeded in 
> these cases was to first generate an alternative conformation for the problem 
> residues, save the file and then do the mutation and save the mutated file. 
> Then, using an editor, I would cut the alternative conformation from the 
> original residue and paste in the alternate conformation (e.g. conformation 
> B) from mutated residue.
> 
> It is not very elegant, but it works (if coot and refmac cooperate).
> 
> Best, Herman
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board  Im Auftrag von Abhishek Anan
> Gesendet: Sonntag, 26. April 2020 21:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME 
> (met-sulfoxide)
> 
> EXTERNAL : Real sender is  owner-ccp...@jiscmail.ac.uk   
> 
> 
> 
> Dear all,
> 
> Thanks for the suggestions. It is synthetic peptide so the residue identity 
> is unambiguous.
> 
> I am not clear on how to model both MET and SME in coot, do a real space 
> refinement and then save the file for refinement in phenix. I tried alternate 
> conformation and then mutating one of them but that didn't work as both 
> conformations were mutated. What I also just noticed is that the refinement 
> of structure with just SME results in positive densities around all side 
> chain carbons even with the SME.cif loaded into phenix. What could be wrong 
> here?
> 
> best wishes,
> Abhishek
> 
> 
> 
> 
> 
> On 4/26/20, Paul Emsley  wrote:
>> 
>> On 26/04/2020 16:21, Abhishek Anan wrote:
>>> Dear all,
>>> 
>>> I have a peptide crystal structure at 0.97 Å that contains two 
>>> surface exposed Methionine. The CE atoms of both MET have a 
>>> suspiciously high b-factor >40 and a positive density. In addition, 
>>> the sulfur atom SD has a large negative density (b-factor ~23).
>>> 
>>> I initially suspected that the MET may have oxidized to MET-sulfoxide 
>>> and tried to model only the MET-sulfoxide. This again resulted in 
>>> negative density.
>>> 
>>> I think that the peptides might be partly oxidized which brings me to 
>>> my question. Is there a way to model both MET and MET-sulfoxide into 
>>> the density much like alternate conformation with options to refine 
>>> their respective occupancies.
>> 
>> 
>> Yes. This is called micro-heterogeneity
>> 
>> And is documented here:
>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.wwpdb.org_doc
>> umentation_procedure=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5
>> qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=CYQUM_mrfiCDADJ1
>> onMNLQYYLwXD23pcMOTm7KnoNkM=A_ke05wSRD1nm9vQxFwLPCzpmUAWRTVlaVkVSTRw
>> z8M=
>> 
>> That should "just work" if you then give the model to refmac.
>> 
>> FWIW, Coot is, AFAIR, not 100% happy with such models.
>> 
>> Paul.
>> 
>> 
>> 
> 
> 
> 
> 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_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=CYQUM_mrfiCDADJ1onMNLQYYLwXD23pcMOTm7KnoNkM=6ogarHdS3ZYDDHIOFlsDYS2crwXpeNiaY2wIG_dXsEA=
> 
> 
> 
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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)

[Schreuder, Herman /DE]

Dear Abhishek,

I did not follow the links given by Paul. However the way I proceeded in these 
cases was to first generate an alternative conformation for the problem 
residues, save the file and then do the mutation and save the mutated file. 
Then, using an editor, I would cut the alternative conformation from the 
original residue and paste in the alternate conformation (e.g. conformation B) 
from mutated residue.

It is not very elegant, but it works (if coot and refmac cooperate).

Best, Herman

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Abhishek Anan
Gesendet: Sonntag, 26. April 2020 21:42
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME 
(met-sulfoxide)

EXTERNAL : Real sender is  owner-ccp...@jiscmail.ac.uk   



Dear all,

Thanks for the suggestions. It is synthetic peptide so the residue identity is 
unambiguous.

I am not clear on how to model both MET and SME in coot, do a real space 
refinement and then save the file for refinement in phenix. I tried alternate 
conformation and then mutating one of them but that didn't work as both 
conformations were mutated. What I also just noticed is that the refinement of 
structure with just SME results in positive densities around all side chain 
carbons even with the SME.cif loaded into phenix. What could be wrong here?

best wishes,
Abhishek





On 4/26/20, Paul Emsley  wrote:
>
> On 26/04/2020 16:21, Abhishek Anan wrote:
>> Dear all,
>>
>> I have a peptide crystal structure at 0.97 Å that contains two 
>> surface exposed Methionine. The CE atoms of both MET have a 
>> suspiciously high b-factor >40 and a positive density. In addition, 
>> the sulfur atom SD has a large negative density (b-factor ~23).
>>
>> I initially suspected that the MET may have oxidized to MET-sulfoxide 
>> and tried to model only the MET-sulfoxide. This again resulted in 
>> negative density.
>>
>> I think that the peptides might be partly oxidized which brings me to 
>> my question. Is there a way to model both MET and MET-sulfoxide into 
>> the density much like alternate conformation with options to refine 
>> their respective occupancies.
>
>
> Yes. This is called micro-heterogeneity
>
> And is documented here:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.wwpdb.org_doc
> umentation_procedure=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5
> qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=CYQUM_mrfiCDADJ1
> onMNLQYYLwXD23pcMOTm7KnoNkM=A_ke05wSRD1nm9vQxFwLPCzpmUAWRTVlaVkVSTRw
> z8M=
>
> That should "just work" if you then give the model to refmac.
>
> FWIW, Coot is, AFAIR, not 100% happy with such models.
>
> Paul.
>
>
>



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