- phenixbb - phenix-online.org

restraints_edits.params -- inquiries -- issues
by p.auffinger 30 Mar '23

30 Mar '23

Hi phenix users, I started to add restraints to a large ribosomal file by using the file (in full) below. I encountered two issues: 1) The first one is: how to use this file in the GUI? It seems to get rejected while its accepted when I run phenix through the command line. 2) The second is: restraints involving water molecules with residue numbers > 9999 get rejected. Could that limit be overcome through a future patch? ### refinement.geometry_restraints.edits { MG_8078 = chain 0 and resname MG and resid 8078 and name MG W_12641 = chain 0 and resname HOH and resid 12641 and name O bond { action = *add atom_selection_1 = $MG_8078 atom_selection_2 = $W_12641 symmetry_operation = None distance_ideal = 2.2 sigma = 0.1 slack = None } } ### Thanks for any thoughts on this, Pascal ----- Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffinger(a)ibmc-cnrs.unistra.fr -----

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27th Annual SCSB Structural Biology Symposium - Registration NOW OPEN
by White, Mark 21 Mar '23

21 Mar '23

You and your colleagues are cordially invited to join us for the 27th Annual Structural Biology Symposium to be held on April 29, 2023 in Levin Hall, UTMB Galveston. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. This year’s speakers include: Yunfeng Chen Ph.D. Univ. of Texas Medical Branch Ruben L. Gonzalez Jr., Ph.D. Columbia University John A. Tainer, Ph.D. University of Texas MD Anderson Cancer Center David W. Taylor, Ph.D. University of Texas Junjie Zhang Ph.D. Texas A&M University To register or for more information, visit https://scsb.utmb.edu/symposium Mark Andrew White, Ph.D. Associate Professor of Biochemistry & Molecular Biology, UTMB, Galveston, TX 409.747.4747 https://xray.utmb.edu ________________________________

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Save the date! “Not the GRC” on Diffraction Methods in Structural Biology 2024
by Winter, Graeme (DLSLtd,RAL,LSCI) 17 Mar '23

17 Mar '23

Good afternoon all, “Not the Gordon Research Conference” on Diffraction Methods in Structural Biology 2024 - Experiments and Measurements Organisers: Graeme Winter, Kunio Hirata (NTGRC-chairs) Helena Taberman, Ali Ebrahim (NTGRS-chairs) Local organisers - Arwen Pearson, Ashwin Chari As you will have seen from a message from James Holton last year, the GRC have decided that the 2024 meeting on Diffraction Methods will not be further supported. We are not deterred! A number of the GRC ex-chairs and those nominated for chairing the next meeting feel that this opportunity for the diffraction methods community to come together is important enough that it should continue to happen, even without GRC support. We are therefore delighted to launch the “Not-the-GRC Diffraction methods in Structural Biology”. The topic of the meeting will be “Experiments and Measurements” and we have a great lineup of speakers in mind. Where: https://www.harnackhaus-berlin.mpg.de/en When: 21st - 27th July 2024 i.e. about when the next diffraction methods meeting would have been. Starting with the model of the GRC, since we collectively believe it is a fantastic meeting, we plan to make a few improvements (better accommodation and acoustics, fewer minimum attendees to keep the feel of a small meeting) and we will keep the equivalent of the GRS before the main meeting, as well as the free afternoons for collaborative discussion, and the strong emphasis on being able to talk to everyone. We will also keep the focus on new ideas and so follow the protocol of not recording presentations and encouraging the presentation of unpublished data and ideas. With that in mind, this will be a small meeting (100-120 maximum) so there will be an application process and we will open registration in January 2024. We also want as many early career people as possible - the last GRC was refreshing and fun with a lot of new faces, and this is something we want to build on. So, please hold the date in your calendar and we look forward to sharing the scientific programme with you in the coming months and seeing many of you in Berlin next summer. All the best Graeme, Kunio, Helena, Ali, Arwen and Ashwin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Postdoc positions in cryo-EM development at the MRC Laboratory of Molecular Biology, Cambridge UK
by Jan Löwe 13 Mar '23

13 Mar '23

*Postdoctoral positions available in cryo-EM methods development at the MRC Laboratory of Molecular Biology, Cambridge UK, in the groups of Chris Russo and Jan Löwe* We have one position each available, funded for two years as part of the LMB’s Blue Sky collaboration with AstraZeneca. The project, in collaboration with Kasim Sader at AZ aims to develop novel methods to overcome problems with sample denaturation and preferred orientation during vitrification of thin aqueous films. Ideas involve outrunning the processes involved and modifying the air-water interfaces. The ultimate goal is to make cryo-EM sample preparation a much more universal (and enjoyable) process. Cryo-EM experience will be beneficial and a strong desire to engage deeply in technical developments is a must. The LMB and AZ provide everything required, including a highly collaborative and friendly environment, as well as one of the world’s best institutional cryo-EM setups, including state-of-the-art machine and electronics workshops, a clean room dedicated to grid fabrication, and soon four Titan Krios microscopes. More details and on how to apply are here: https://www.nature.com/naturecareers/job/12796284/postdoctoral-scientist-st… https://www.nature.com/naturecareers/job/12796280/postdoctoral-scientist-st… Chris, Kasim and Jan Jan Löwe MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK Email: jyl(a)mrc-lmb.cam.ac.uk Phone +44 1223 26 7644 Website: http://www2.mrc-lmb.cam.ac.uk/groups/jyl Christopher J Russo  MRC Laboratory of Molecular Biology  Cambridge, CB2 0QH, UK Email: crusso(a)mrc-lmb.cam.ac.uk  Phone +44 1223 26 7535 Website http://www.mrc-lmb.cam.ac.uk/crusso/

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Local restraints
by Luca Pellegrini 07 Mar '23

07 Mar '23

How can I freeze a set of atoms in phenix.real_space_refine? I've got an arginine side chain that is consistently misplaced during refinement, and I’d like to restrain its movement. I notice that refinement.geometry_restraints.edits.scale_restraints is not available anymore, is there another way? Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Two postdoctoral positions at CNB-CSIC, Spain
by Carmen San Martin 23 Feb '23

23 Feb '23

Dear all, Please find here information on two open positions on structural biology / protein design: https://saco.csic.es/index.php/s/gFm9EKLMNBWD2G8 Regards, ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 (internal: 432228) Fax: 34-91-5854506 <http://www.cnb.csic.es/> http://wwwuser.cnb.csic.es/~sanmartinlab http://www.microscopia.org ------------------------------------------------------------

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Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023
by Armando Albert 20 Feb '23

20 Feb '23

Dear all, The registration for the next edition of the Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023 is open. The workshop has been organized at Instituto de Química Física Rocasolano CSIC since 2010 and it is meant for 25 graduate students or researchers with previous expertise in crystallography and/or CryoEM who need a deeper insight into the most advanced crystallographic and CryoEM techniques to carry out their research projects. The program traditionally covers aspects such as sample preparation, structure solution, model building, crystallographic refinement, validation, and analysis of the structural results, as well as an overview of the newest structural biology technologies. On top of these subjects, this year's program will include those aspects related to the impact of Artificial Intelligence methods on structure solution and low-resolution refinement. In addition, we will cover dynamic crystallography at XFEL and synchrotron and ligand building for drug discovery. You may find further information on our website (https://www.xtal.iqfr.csic.es/MCCS2023/index.html <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2…>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento de Cristalografía y Biología Estructural Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas Serrano 119, 28006 Madrid Spain

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(no subject)
by Armando Albert 06 Feb '23

06 Feb '23

Dear all, The registration for the next edition of the Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023 is open. The workshop has been organized at Instituto de Química Física Rocasolano CSIC since 2010 and it is meant for 25 graduate students or researchers with previous expertise in crystallography and/or CryoEM who need a deeper insight into the most advanced crystallographic and CryoEM techniques to carry out their research projects. The program traditionally covers aspects such as sample preparation, structure solution, model building, crystallographic refinement, validation, and analysis of the structural results, as well as an overview of the newest structural biology technologies. On top of these subjects, this year's program will include those aspects related to the impact of Artificial Intelligence methods on structure solution and low-resolution refinement. In addition, we will cover dynamic crystallography at XFEL and synchrotron and ligand building for drug discovery. You may find further information on our website (https://www.xtal.iqfr.csic.es/MCCS2023/index.html <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2…>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento de Cristalografía y Biología Estructural Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas Serrano 119, 28006 Madrid Spain

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Solving MR solution without sequence information
by Rosenberg, Eric (NIH/NCI) [F] 06 Feb '23

06 Feb '23

Hi all, I'm in a bit of bind here and am seeking some advice. For context, a former graduate student in our lab set crystal trays of an MBP fusion protein, the fused part after MBP being ~400 amino acids long. This region is also predicted to be mostly unstructured, but has a C-terminal SH3 domain. Our graduate student then graduated and before throwing out some of her trays a year or two later, we found some hits of the MBP fusion protein that actually diffracted to 2.9 Angstrom. I spent some time working on it after we collected the data (June 2021), but because I didn't know what crystallized specifically, it was impossible to phase, and replicating seemed next to impossible, too. The Matthew's coefficient was predicting ~130 amino acids in the ASU, space group C222 or C2221. Since whatever crystallized was clearly a degradation product of the MBP fusion, I tried phasing with SH3 domains and a lot of other things to no avail. As a final last ditch effort I eventually submitted the .mtz file to SBGrid to perform a Wide Search MR job, and low and behold it actually found MR solutions that had TFZ scores ~17 in space group C2221! So here's my current situation-I have been able to phase the data set using the MR search model, but again, I don't know what specifically it is that I've crystallized. I'm currently able to get the Rfree to ~0.4, but can't seem to improve it. I am really at a loss of what to do, since there are obvious backbone issues with the protein (as seen from iterative build composite omit maps), but every time I try to manually correct them it seems to make the Rfree worse. The MR solution does not align very well at all to the MBP fusion, only ~20 identity, and again, I don't know to which ~130 amino acids I crystallized out of the ~400 of the MBP fusion. Is it one continuous stretch, two copies of a shorter stretch, etc.? I tried phasing with a polyalanine model of the MR search model and then tried autobuilding just a polyalanine sequence to get the backbone right, but that doesn't seem to work. Autobuild also fails when trying to various fragments of the MBP fusion sequence. Other than opening coot and manually building the entire polypeptide chain, is there an easier method? I think that once the backbone is totally right the phases will improve so I can start putting in side chains, but I'm not sure. My latest effort is to just use Sculptor prior to Phaser in order to force the sequences to match, but again, I don't know precisely what sequence was crystallized. I have tried both the Phenix and CCP4 software suites, for reference. Any and all help would be much appreciated (and yield an acknowledgement on a paper, if this ever works). Best, Eric Rosenberg CRTA Postdoctoral Fellow Randazzo Lab Laboratory of Cellular and Molecular Biology National Cancer Institute, US

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Re: [phenixbb] Solving MR solution without sequence information
by Dom Bellini 04 Feb '23

04 Feb '23

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