Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

[Alejandro Buschiazzo]

Thank you for your comment, we cannot agree more.

We are aware of this, and still are in the process of inviting a few more 
speakers. 
We shall  thus bring more  women on board, and achieve a balanced group!

Cheers,
Alejandro (on behalf of the organizers)


El 4 feb. 2020, a la(s) 22:02, Edward Snell  escribió:

> ​It is great that this workshop is occurring but I couldn't help but notice 
> that there seem to be a lot of male speakers and tutors. I was wondering if 
> it might be appropriate to add some female role models. There are some great 
> candidates?
> 
> 
> 
> 
> 
>  
> From: CCP4 bulletin board  on behalf of Alejandro 
> Buschiazzo 
> Sent: Tuesday, February 4, 2020 7:30 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Macromolecular Crystallography workshop in South America 
> 2020
>  
> Dear colleagues,
> 
> We are pleased to announce the 8th South American Macromolecular 
> Crystallography School: 
> 
> Macromolecular Crystallography School 2020 
> 
> "Structural Biology to enhance high impact research in health and disease”
> 
> 
> To be held at the Institut Pasteur de Montevideo (Uruguay) - September 9-19, 
> 2020
> http://pasteur.uy/novedades/mx2020/
> 
> 
> The application deadline is July 9, 2020. For further inquiries : 
> mx2...@pasteur.edu.uy
> 
> 
> Main Topics:
> 
> ·   data processing;
> 
> ·   phasing and structure determination;
> 
> ·   model refinement and validation;
> 
> ·   introduction to crystallography + cryo-electron microscopy integration
> 
> 
> Confirmed speakers and tutors (so far... a few more will join the crew): 
> 
> 
> Alejandro Buschiazzo (Institut Pasteur de Montevideo, Uruguay)
> 
> Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK)
> 
> Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil)
> 
> Ronan Keegan (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
> 
> Eugene Krissinel (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
> 
> Joāo Muniz (Instituto de Fisica de São Carlos, Brazil)
> 
> Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK)
> 
> Colin Palmer (STFC Rutherford Appleton Lab - CCP-EM, Didcot, UK)
> 
> James Parkhurst (Diamond Light Source, Didcot, UK)
> 
> Randy Read (University of Cambridge, UK)
> 
> Kyle Stevenson (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
> 
> Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK)
> 
> 
> Please find the application form and further contact information at 
> http://pasteur.uy/novedades/mx2020/ 
> (this www site will be updated regularly, so stay tuned!)
> 
> 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.
> 
> Organizers:
> Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay
> Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United 
> Kingdom
> Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil
> 
> Applicants:
> 25 students will be selected, prioritizing advanced PhD, postdocs and young 
> researchers. The Course will provide financial support covering registration 
> fees, and for the case of those students coming from abroad, all local 
> expenses (lodging, per diem and local transportation). Look in the www site 
> for details on application procedures.
> 
> The application deadline is July 9, 2020.
> 
> Please address further inquiries to: mx2...@pasteur.edu.uy
> 
> Looking forward to hosting you in Montevideo!
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

[Edward Snell]

?It is great that this workshop is occurring but I couldn't help but notice 
that there seem to be a lot of male speakers and tutors. I was wondering if it 
might be appropriate to add some female role models. There are some great 
candidates?




From: CCP4 bulletin board  on behalf of Alejandro 
Buschiazzo 
Sent: Tuesday, February 4, 2020 7:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Dear colleagues,

We are pleased to announce the 8th South American Macromolecular 
Crystallography School:

Macromolecular Crystallography School 2020
"Structural Biology to enhance high impact research in health and disease"

To be held at the Institut Pasteur de Montevideo (Uruguay) - September 9-19, 
2020
http://pasteur.uy/novedades/mx2020/

The application deadline is July 9, 2020. For further inquiries : 
mx2...@pasteur.edu.uy


Main Topics:

*   data processing;

*   phasing and structure determination;

*   model refinement and validation;

*   introduction to crystallography + cryo-electron microscopy integration

Confirmed speakers and tutors (so far... a few more will join the crew):

Alejandro Buschiazzo (Institut Pasteur de Montevideo, Uruguay)
Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK)
Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil)
Ronan Keegan (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
Eugene Krissinel (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
Joao Muniz (Instituto de Fisica de São Carlos, Brazil)
Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK)
Colin Palmer (STFC Rutherford Appleton Lab - CCP-EM, Didcot, UK)
James Parkhurst (Diamond Light Source, Didcot, UK)
Randy Read (University of Cambridge, UK)
Kyle Stevenson (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)
Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK)

Please find the application form and further contact information at 
http://pasteur.uy/novedades/mx2020/
(this www site will be updated regularly, so stay tuned!)

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.

Organizers:
Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay
Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom
Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil

Applicants:
25 students will be selected, prioritizing advanced PhD, postdocs and young 
researchers. The Course will provide financial support covering registration 
fees, and for the case of those students coming from abroad, all local expenses 
(lodging, per diem and local transportation). Look in the www site for details 
on application procedures.

The application deadline is July 9, 2020.

Please address further inquiries to: 
mx2...@pasteur.edu.uy

Looking forward to hosting you in Montevideo!



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] Macromolecular Crystallography workshop in South America 2020

[Alejandro Buschiazzo]

Dear colleagues,

We are pleased to announce the 8th South American Macromolecular 
Crystallography School: 

Macromolecular Crystallography School 2020 

"Structural Biology to enhance high impact research in health and disease”


To be held at the Institut Pasteur de Montevideo (Uruguay) - September 9-19, 
2020
http://pasteur.uy/novedades/mx2020/


The application deadline is July 9, 2020. For further inquiries : 
mx2...@pasteur.edu.uy 


Main Topics:

·   data processing;

·   phasing and structure determination;

·   model refinement and validation;

·   introduction to crystallography + cryo-electron microscopy integration


Confirmed speakers and tutors (so far... a few more will join the crew): 


Alejandro Buschiazzo (Institut Pasteur de Montevideo, Uruguay)

Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK)

Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil)

Ronan Keegan (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)

Eugene Krissinel (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)

Joāo Muniz (Instituto de Fisica de São Carlos, Brazil)

Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK)

Colin Palmer (STFC Rutherford Appleton Lab - CCP-EM, Didcot, UK)

James Parkhurst (Diamond Light Source, Didcot, UK)

Randy Read (University of Cambridge, UK)

Kyle Stevenson (STFC Rutherford Appleton Lab - CCP4, Didcot, UK)

Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK)


Please find the application form and further contact information at 
http://pasteur.uy/novedades/mx2020/ 
(this www site will be updated regularly, so stay tuned!)

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.

Organizers:
Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay
Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom
Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil

Applicants:
25 students will be selected, prioritizing advanced PhD, postdocs and young 
researchers. The Course will provide financial support covering registration 
fees, and for the case of those students coming from abroad, all local expenses 
(lodging, per diem and local transportation). Look in the www site for details 
on application procedures.

The application deadline is July 9, 2020.

Please address further inquiries to: mx2...@pasteur.edu.uy 


Looking forward to hosting you in Montevideo!


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

[ccp4bb] Crystallography position at Evotec in the Structural Biology group

[Stephanie Duclos]

Dear CCP4 community,

This is just a refresher, we are still looking to recruit 4 crystallographers.



Evotec (UK) Ltd is currently seeking to add to our Structural Biology 
Department.  The group works closely with our Discovery Chemistry Department 
and with clients to develop novel small molecule drugs.  The group is at the 
forefront of new science and technology, and is seeking to expand as business 
needs grow.
If you are interested, please apply using this link:
https://evotecgroup.wd3.myworkdayjobs.com/Evotec_Career_Site/job/Abingdon-Evotec/Senior-Crystallography-Scientist_REQ-01410

Best regards,
Stephanie


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privileged and/or private information.  
If received in error, please notify us immediately by reply email and then 
delete this email and any attachments from your system. Thank you!


https://www.evotec.com/en/about/site-information/data-protection-uk

Evotec (UK) Ltd is a limited company registered in England and Wales. 
Registration number:2674265. Registered office: 114 Innovation Drive, Milton 
Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom.



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[ccp4bb] PhD student position at CBI/IGBMC Strasbourg

[Mikhail ELTSOV]

Ph.D. student position in cryo-electron tomography

A PhD position is available in Mikhail Eltsov’s team at the CBI/IGBMC to study 
chromatin structure-based mechanisms of epigenetic silencing 
(http://www.igbmc.fr/igbmc/recrutement/job_offer/505/).
IGBMC - Offre d'emploi PHD
www.igbmc.fr
Institut de Génétique et de Biologie Moléculaire et Cellulaire


The CBI provides a leading-edge scientific and technological environment in 
integrated structural biology to address the structure and function of 
biological systems, notably on gene expression, from the atomic, molecular to 
the tissue scales. The CBI http://www.igbmc.fr/grandesstructures/cbi/, hosts 
the French and European Infrastructures for Integrated Structural Biology, 
FRISBI http://frisbi.eu/, Instruct-ERIC https://www.structuralbiology.eu/ and 
iNext-Discovery 
https://instruct-eric.eu/news/eu-inext-discovery-grant-provides-technologies-for-key-research-in-structural-biology/,
 which comprises advanced electron microscopy facilities equipped with 
cutting-edge instrumentation such as Titan Krios and Polara cryo electron 
microscopes, cryo Focused Ion Beam Scanning Electron Microscope (FIB/SEM) and 
super-resolution fluorescence microscopy 
http://frisbi.eu/centers/instruct-center-france-1-igbmc/cryo-electron-microscopy/.
 The Titan Krios microscope is equipped with Cs corrector, Falcon 3 camera, GIF 
energy filter, K3 camera and phase plate. The installation of a high-end 
screening microscope is planned during 2020. In addition, the EM facility has a 
suite of associated equipments for sample preparation and dedicated computing 
resources for image processing and 3D reconstruction by single particle cryo-EM 
and cryo electron tomography (cryo-ET) and software developements. For projects 
and publications of the associated teams see 
http://www.igbmc.fr/research/department/3/

For details of the project and other enquiries, please contact Prof. Mikhail 
Eltsov. To apply, please email your motivational letter, CV, copies of your 
university degrees and names of referees to mikhail.elt...@igbmc.fr

--

Mikhail Eltsov

Professor of Structural Biology

Centre for Integrative Biology

Department of Integrated Structural Biology

Institute of Genetics and of Molecular and Cellular Biology

IGBMC - UMR 7104 - U 1258

1, rue Laurent Fries

67404 ILLKIRCH CEDEX

FRANCE

http://www.igbmc.fr/research/department/3/team/138/




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Re: [ccp4bb] refinement of 0.73A data in shelxl

[00000c2488af9525-dmarc-request]

Thanks, sorry, shelx is wonderful! I was thinking back to shelxpro days when your hetero-atoms could acquire the wrong scattering factors if they were not positioned right in the pdb file. The classic, which I saw several times, was calcium (CA) being treated as an alpha-carbon (CA), and I think refmac and others probably still do this if the PDB-standard leftward offset of the atom type is not present.Jon CooperOn 4 Feb 2020 08:24, Tim Gruene  wrote:Dear Jon,

in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you like. 
The scattering factor is derived from the number next to the name. The name is 
just that, and identifier.

Best,
Tim

On Monday, February 3, 2020 9:20:03 PM CET 0c2488af9525-dmarc-
requ...@jiscmail.ac.uk wrote:
> Remembered earlier that if the "CL" is not shifted one place to the left,
> Shelx and probably most other programs treat it as carbon, i.e. its assumed
> to have 6 rather than 17 electrons. Trust occupancies OK, too ;-?
> 
> 
> Jon Cooper
> 
> 
> On 3 Feb 2020 18:26, "Barone, Matthias"  wrote:
> 
> 
> Hi Pavel
> 
> glad you write me. I was hoping you would read my post.
> 
> - Yes, protons are added, both on the protein as well as on the molecule
> 
> - I initially only refined protein and ligand anisotropically, now Im
> running a refinement with all atoms anisotrp except Hs. This would then
> also be the same as shelxl is doing.
> 
> - Alternate conformations are modeled, also on the ligand. There are plenty,
> sure, but I think I got most of them.
> 
> - I already used Water update during refine, there are some NO3s in the
> structure. I got them in. There is a second ligand somewhere as artifact.
> its density is not well defined, so I hope to get that in once the map
> clears up more. 
> 
> - I let phenix.refine optimize adp and chemisty weights, but as Petri
> suggested, Im manually increasing the scale factors to match the ones from
> shelxl (just to compare them properly). Im aiming for an rsmd of 0.02-0.03A
> like Petri suggested and keep an eye on how tight the structure is refined
> in shelxl.
> 
> 
> 
> 
> About the Rfact and the gap. Yes, thats what I was expecting. I hope if I
> add more anisotropic B fact, the Rfacts should go down to at least what
> shelxl yielded. 
> 
> 
> 
> 
> thank you all again for the massive feedback, ideas and help. 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> 
> From:Pavel Afonine 
> Sent:Monday, February 3, 2020 7:14:25 PM
> To:Barone, Matthias
> Cc:CCP4BB@JISCMAIL.AC.UK
> Subject:Re: [ccp4bb] refinement of 0.73A data in shelxl
>  
> Hi Matthias,
> 
> 
> did you use correct model parameterization and optimal refinement strategy
> for the resolution? Such as: - Add H atoms;
> - Refine all but H atoms with anisotropic ADPs;
> - Model alternative conformations (that one'd expect many at this
> resolution); - Add solvent (water, crystallization cocktail components if
> you see any); - Relax restraints on geometry and ADPs;
>  long list!
> 
> 
> If not, then what you have in terms of R factors is more or less what I'd
> expect.
> 
> 
> In the absence of obvious data pathologies, I'd expect Rwork/Rfree in 10-15%
> range, and the Rfree-Rwork gap around 1-2% or less.
> 
> 
> Since you mentioned Phenix refinement, I am happy to help you with details
> etc off-list.
> 
> 
> Pavel
> 
> 
> On Mon, Feb 3, 2020 at 3:08 AM Barone, Matthias 
> wrote:
> 
> 
> Dear ccp4 community
> 
> Im having some problems solving a 0.73A structure. Spacegroup seems to be
> correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer
> shell CC1/2 24% and 90.4% complete.
> 
> The model is nearly fully built, there is no remaining unmodelled areas.
> However, Rfactisstuck 27% in phenix, with a very distinct artifact in the
> electron map (see phenix.jpg). You can see difference density on various
> well defined sidechain atoms. Notably, they seem to follow a pattern:
> Nearly all Val CG have difference signal, as well as many backbone
> NH. Hence, I suspected that it might be a problem with the SF, since we
> recorded the DS at 0.86A.
> 
> 
> 
> 
> Hence I gave shelxl a shot:
> 
> I used the refined model from phenix, converted it via pdb2ins and pasted
> the restraints created by prodrg. 
> 
> The shelxl hkl was produced by xdsconv, using the freeR flagging of the mtz
> used by phenix (no merge, friedel false).
> 
> Interestingly, shelxl can bring Rfree down to 16% and almost all of
> the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg).
> Except one: the inhibitor contains a chlorinated phenylring (pdb ligand
> 2L5) which now shows massive difference density for Cl.

[ccp4bb] Structural biology - PhD positions available

[Demo, Gabriel]

Hi everyone,

I have two PhD. positions available in my newly established lab at the Central 
European Institute of Technology (CEITEC) Masaryk University in Czech Republic.

We are seeking students who are interested in determining structures of coupled 
transcription-translation complexes using cryo-EM and cryo-ET. The candidates 
should have a good background in biochemistry or structural biology and some 
experience with single-particle cryo-electron microscopy or cryo-electron 
tomography.

For more details look here:
https://www.ceitec.eu/structural-biology-of-coupled-transcription-translation-gabriel-demo/rg352/tab?tabId=129


All best,

--
Gabriel Demo, PhD.
Masaryk University, CEITEC
625 00 Brno, Czech Republic

and

UMass Medical Shool, RTI
Korostelev lab
01605, Worcester, USA

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[ccp4bb] Marie Curie fellowships hosted at the Arctic University of Norway

[Richard Alan Engh]

Dear crystallographers et al,

UiT the Arctic University of Norway sponsors applicants for Marie 
Skƚodowska-Curie individual fellowships hosted in Tromsø, Norway, including the 
Norwegian Structural Biology Center. Applicants chosen for sponsorship will be 
invited to an application writing seminar in May, please see information at 
this address:

https://euraxess.ec.europa.eu/jobs/480181

Applicants need not be specialists in crystallography to apply, but must show 
how a two-year postdoctoral research program in structural biology and 
structure based drug design will expand their skills and further their careers. 
For initial selection, the candidate must show a strong CV and sketch a brief 
and relevant research plan.

NOTE: The deadline for the initial phase of this process is very soon:  Friday, 
7. February!

Thank you CCP4BB readers for passing this information on to potentially 
interested PhD scientists.

Sincerely,
Rick Engh




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Re: [ccp4bb] Refmac5 question

[Robbie Joosten]

Hi Joern,

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

Cheers,
Robbie 

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

[Huw Jenkins]

> On 4 Feb 2020, at 09:24, Joern Krausze  wrote:
> 
> These hydrogen atoms were present in the input file with their occupancies 
> matching that of the residues they are attached to. 

What happens with make hydrogen YES?

That should keep all hydrogens present in the input file 
(http://www.ccp4.ac.uk/html/refmac5/keywords/restraints.html#make_hydr)


Huw



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[ccp4bb] Refmac5 question

[Joern Krausze]

Dear all,

I've got a Refmac5 question. When I refine my protein structure in 
Refmac5 with the options make hydrogen ALL and make hout yes, some of 
the hydrogen atoms in the output file have zero occupancies. At a first 
glance, only the the H-atoms attached to OG1 of Ser, ND2 of Asn, and NE2 
of Gln are affected. These hydrogen atoms were present in the input file 
with their occupancies matching that of the residues they are attached 
to. Is there a reason for this behavior that I might be missing? I am 
currently running Refmac version 5.8.025.



Best regards,

Joern

--
*
Address:

Joern Krausze
Department of Plant Biology
Braunschweig University of Technology
Spielmannstr. 7
38106 Braunschweig
Germany

Email:  j.krau...@tu-braunschweig.de
Phone:  +49 (0)531 3915858
*




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Re: [ccp4bb] refinement of 0.73A data in shelxl

[Tim Gruene]

Dear Jon,

in SHELX(L), you can name your atoms foo and bar, or jon and doe, if you like. 
The scattering factor is derived from the number next to the name. The name is 
just that, and identifier.

Best,
Tim

On Monday, February 3, 2020 9:20:03 PM CET 0c2488af9525-dmarc-
requ...@jiscmail.ac.uk wrote:
> Remembered earlier that if the "CL" is not shifted one place to the left,
> Shelx and probably most other programs treat it as carbon, i.e. its assumed
> to have 6 rather than 17 electrons. Trust occupancies OK, too ;-?
> 
> 
> Jon Cooper
> 
> 
> On 3 Feb 2020 18:26, "Barone, Matthias"  wrote:
> 
> 
> Hi Pavel
> 
> glad you write me. I was hoping you would read my post.
> 
> - Yes, protons are added, both on the protein as well as on the molecule
> 
> - I initially only refined protein and ligand anisotropically, now Im
> running a refinement with all atoms anisotrp except Hs. This would then
> also be the same as shelxl is doing.
> 
> - Alternate conformations are modeled, also on the ligand. There are plenty,
> sure, but I think I got most of them.
> 
> - I already used Water update during refine, there are some NO3s in the
> structure. I got them in. There is a second ligand somewhere as artifact.
> its density is not well defined, so I hope to get that in once the map
> clears up more. 
> 
> - I let phenix.refine optimize adp and chemisty weights, but as Petri
> suggested, Im manually increasing the scale factors to match the ones from
> shelxl (just to compare them properly). Im aiming for an rsmd of 0.02-0.03A
> like Petri suggested and keep an eye on how tight the structure is refined
> in shelxl.
> 
> 
> 
> 
> About the Rfact and the gap. Yes, thats what I was expecting. I hope if I
> add more anisotropic B fact, the Rfacts should go down to at least what
> shelxl yielded. 
> 
> 
> 
> 
> thank you all again for the massive feedback, ideas and help. 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> 
> From:Pavel Afonine 
> Sent:Monday, February 3, 2020 7:14:25 PM
> To:Barone, Matthias
> Cc:CCP4BB@JISCMAIL.AC.UK
> Subject:Re: [ccp4bb] refinement of 0.73A data in shelxl
>  
> Hi Matthias,
> 
> 
> did you use correct model parameterization and optimal refinement strategy
> for the resolution? Such as: - Add H atoms;
> - Refine all but H atoms with anisotropic ADPs;
> - Model alternative conformations (that one'd expect many at this
> resolution); - Add solvent (water, crystallization cocktail components if
> you see any); - Relax restraints on geometry and ADPs;
>  long list!
> 
> 
> If not, then what you have in terms of R factors is more or less what I'd
> expect.
> 
> 
> In the absence of obvious data pathologies, I'd expect Rwork/Rfree in 10-15%
> range, and the Rfree-Rwork gap around 1-2% or less.
> 
> 
> Since you mentioned Phenix refinement, I am happy to help you with details
> etc off-list.
> 
> 
> Pavel
> 
> 
> On Mon, Feb 3, 2020 at 3:08 AM Barone, Matthias 
> wrote:
> 
> 
> Dear ccp4 community
> 
> Im having some problems solving a 0.73A structure. Spacegroup seems to be
> correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer
> shell CC1/2 24% and 90.4% complete.
> 
> The model is nearly fully built, there is no remaining unmodelled areas.
> However, Rfactisstuck 27% in phenix, with a very distinct artifact in the
> electron map (see phenix.jpg). You can see difference density on various
> well defined sidechain atoms. Notably, they seem to follow a pattern:
> Nearly all Val CG have difference signal, as well as many backbone
> NH. Hence, I suspected that it might be a problem with the SF, since we
> recorded the DS at 0.86A.
> 
> 
> 
> 
> Hence I gave shelxl a shot:
> 
> I used the refined model from phenix, converted it via pdb2ins and pasted
> the restraints created by prodrg. 
> 
> The shelxl hkl was produced by xdsconv, using the freeR flagging of the mtz
> used by phenix (no merge, friedel false).
> 
> Interestingly, shelxl can bring Rfree down to 16% and almost all of
> the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg).
> Except one: the inhibitor contains a chlorinated phenylring (pdb ligand
> 2L5) which now shows massive difference density for Cl.
> 
> I therefore suggested that I might deal with a wrong SF for Cl. Funny
> enough, pdb2ins does not produce a DISP line for Cl if converting the pdb
> that contains the inhibitor. Hence, I used pdb2ins and the pdb from PRODRG
> to produce SFAC for the inhibitor Cloride. I then pasted this line
> 
> 
> DISP $CL0.188450.21747   1035.16450
> 
> 
> 
> into the .res file and updated the UNIT line. Shelxl runs through, and the
> density looks ok on the Chloride now. However Rfree is back up at 24% and
> the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg): now,
> very