- phenixbb - phenix-online.org

Bursaries available for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 25 Oct '24

25 Oct '24

Standard Student Bursaries As in year’s past, CCP4 has made funding available for students, to help with the costs of attending Study Weekend, in the form of a bursary. All students are eligible for a standard bursary which covers the registration fee plus one night’s accommodation in halls. Bursaries will be given out to all students registering during the early bird registration period – 26th September to 11th November 2024. Students obtaining a standard bursary will only need to pay for any additional night’s accommodation. Students wishing to stay in the hotel rather than Rutland halls, will have 1 nights accommodation subsidised at the halls rate and will therefore pay a reduced rate for this night. Additional nights accommodation will need to be paid at the standard cost. Please also note that should you obtain a bursary and cancel after the latest cancellation date of 6 December 2024 you WILL be liable to pay.  This is because we have had a number of students obtaining bursaries and then cancelling last minute.  Places can be transferred to other people at no charge.  Travel bursaries Limited funds will also be made available to help pay travel costs for students and young post-docs from non-UK laboratories. Please send a separate letter, signed by your supervisor and stating the expected cost of travel in pounds sterling, to justify applications for travel support. Supervisors are asked to nominate only one candidate from their Laboratory. Delegates are expected to travel by the most economic means possible. Candidates from less favoured regions will be given preference. Applications should be e-mailed to ccp4sw(a)stfc.ac.uk<mailto:[email protected]> : Lauren Giles CCP4 Study Weekend Travel Bursary Applications for travel bursaries need to be in by Thursday 31st October 2024. Regards Karen McIntyre CCP4 Project Administrator CCP4 ED&I Champion UKRI-STFC Rutherford Appleton Laboratory Harwell Campus Didcot OX11 0QX Phone: +44 (0) 1235 44 5790 [cid:[email protected]] STFC is part of UK Research and Innovation, a public body funded by the UK government. For more information visit www.ukri.org<http://www.ukri.org/> [A grey circle with red text Description automatically generated] Affiliatated Member of the Institute for Continuous Improvement in the Public Sector ***Please note I only work part-time – hours are Monday to Thursday 08:30 to 13:30 and Friday 10:30 to 15:30**********

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working with composite models
by Dmitry Semchonok 24 Oct '24

24 Oct '24

Dear Colleagues, We're encountering an issue with composite model refinement and would appreciate your advice. Our scenario: 1. We built two separate models based on two subtracted maps of a single complex. 2. We have a lower-resolution map of the full complex. 3. We merged the two models into the full complex and refined it against the full map. The problem: When refining the merged model against the full map using real-space refinement in Phenix, the clashscore progressively worsens. Has anyone experienced similar issues, or can you offer suggestions on addressing this problem? Thank you for your insights. Best regards, Dmitry

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About cryo-EM map sharpening in Phenix
by Shanti Pal Gangwar 16 Oct '24

16 Oct '24

Hello everyone, I'm working on anisotropic map sharpening in Phenix version 1.21-5207-00 with a cryo-EM map of a multiprotein complex. Should I provide the sequence files for each component individually, or would it be better to compile all the sequences into a single file? In addition, shall I provide the full sequence even if a segment of the protein is not resolved in the map? I would appreciate any advice! Shanti Pal

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AQuaRef - issues with torch-cluster installation
by Martin Malý 16 Oct '24

16 Oct '24

Dear colleagues, I'm trying to install AQuaRef. However, I'm struggling with running `bash config/update_phenix.sh aimnet2` which is part of `bash build_into_phenix.sh aimnet2`. This script wants to install the python package torch-cluster. However, I'm getting the error: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] I'm getting the same error when I tried to install only this package using the command `qrefine.python -m pip install torch-cluster`. I have a laptop with Ubuntu 22.04. I have all the usual development packages installed (build-essential, linux-headers, gcc, g++, ...). According Python, I have libpython3-dev, libpython3.10-dev, python3-dev, python3.10-dev. I can see that qrefine.python has a version of 3.9, so I also installed libpython3.9-dev, python3.9-dev and python3.9-distutils from ppa:deadsnakes/ppa but it did not help. I am also attaching a full log from the torch-cluster installation. It seems that the package torch has been installed successfully in prior. Do you have please an idea what is wrong and how to fix it? Thank you. Martin

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help for the 4.3 A dataset
by princeadam＠163.com 15 Oct '24

15 Oct '24

Dear colleagues, I am currently engaged in an endeavor to unravel the crystal structure through molecular replacement techniques. Regrettably, the resolution attained stands at a rather low mark, approximately 4.3 Angstroms, which poses significant challenges. Despite exhaustive efforts directed towards optimizing the crystal conditions, there has been no discernible improvement in the resolution. The structure in question is confined to a specific domain, and we have at our disposal two distinct conformational models sourced from the PDB database: one derived from X-ray data and the other from Cryo-EM. Our prime objective is to meticulously discern which of these two conformations aligns most accurately with our experimental context. To this end, we have employed both structures (X-ray and Cryo-EM) as templates for molecular replacement, yet the refinement process has hit a roadblock, hindering our progress. We are seeking a collaborator with experience in dealing with low-resolution data to assist in solving the structure. We are open to sharing first or corresponding authorships in the near future for this paper. Warm regards Hui

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NIH would like your input
by Paul Adams 14 Oct '24

14 Oct '24

Dear Colleagues, For those of you in the US, you might want to know that NIH issued a Request for Information about their National Resources and Biomedical Technology Optimization and Dissemination programs: https://www.research.net/r/NRRs_and_Biomedical_Technology_Optimization_and_… Unfortunately, it closes tomorrow, but it is a short form. They are interested in experiences with existing resources, but are most interested in hearing ideas for expanding the programs to new technologies. Currently funded resources can be found here: https://www.nigms.nih.gov/Research/mechanisms/Pages/NIGMS-National-and-Regi… Information about the Biomedical Technology Optimization and Dissemination program can be found here: https://www.nigms.nih.gov/grants/Pages/btod.aspx NIH would appreciate your thoughts about additional technologies that would benefit the community by support through these programs. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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NIH would like your input
by Paul Adams 14 Oct '24

14 Oct '24

Dear Colleagues, For those of you in the US, you might want to know that NIH issued a Request for Information about their National Resources and Biomedical Technology Optimization and Dissemination programs: https://www.research.net/r/NRRs_and_Biomedical_Technology_Optimization_and_… Unfortunately, it closes tomorrow, but it is a short form. They are interested in experiences with existing resources, but are most interested in hearing ideas for expanding the programs to new technologies. Currently funded resources can be found here: https://www.nigms.nih.gov/Research/mechanisms/Pages/NIGMS-National-and-Regi… National Institute of General Medical Sciences nigms.nih.gov Information about the Biomedical Technology Optimization and Dissemination program can be found here: https://www.nigms.nih.gov/grants/Pages/btod.aspx NIH would appreciate your thoughts about additional technologies that would benefit the community by support through these programs. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Building Rosetta for Phenix
by Martin Malý 14 Oct '24

14 Oct '24

Dear colleagues, I am dealing with a low resolution data set (~4 A, protein crystal structure) so I would like to explore phenix.rosetta_refine. I followed the instructions at https://phenix-online.org/documentation/reference/rosetta_install.html . I applied the patch in ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings . After several minutes of compilation (command rosetta.build_phenix_interface), I got an error. I re-run the command to get a log file which I'm attaching. Please don't you have any idea what's wrong? I use Ubuntu 22.04. Thank you. Best regards, Martin

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Temperature shift alters unit cell of insulin: an issue
by Esra A 09 Oct '24

09 Oct '24

Dear Phenix community, I performed a temperature shift data collection for di-hexamer insulin. I collected single crystal data at 100K, 200K, and 300K, respectively After processing the data, I noticed that the unit cell of the 100K dataset is distinct from 200K and 300K. 100K dataset = 78.2182 78.2182 79.3565 90 90 120 (assume that this is di-hexamer) 200K dataset = 78.3157 78.3157 39.6367 90 90 120 (it is hexamer) 300K dataset = 80.7109 80.7109 39.6399 90 90 120 (it is hexamer) Even if I completed the structure determination of 200K and 300K successfully, I couldn't complete the molecular replacement of the 100K dataset due to the "*The composition entered will not fit in the unit cell volume*" error message. I tried every "copies" and "mass" parameter in *automr *script. However, i got the error message every run. I can share with you the mtz and reference pdb file, if needed. Could you help me, please? Where am I making a mistake? Thank you very much. Sincerely, Esra Ayan

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real space refine ADPs
by Leonid Sazanov 08 Oct '24

08 Oct '24

Hi, according to online description phenix.real_space_refine should refine only group ADPs per residue. However, in practice after the run with ADP included in strategy the recent versions refine individual B-factors per atom. They seem to look OK, but I wonder if this is a beta feature or fully implemented by now? Many thanks Leonid -- Prof. Leonid Sazanov FRS Institute of Science and Technology Austria (ISTA) Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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