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Postdoc positions at MRC-LMB & CCPEM/STFC
by Burnley, Tom (STFC,RAL,SC) 25 Sep '20

25 Sep '20

Dear all, For those interesting in computational cryoEM development... We are excited to announce two new PDRA positions in the Scheres’ group (MRC-LMB, UK) and the CCP-EM group (STFC RAL, UK). These two positions will work closely together as part of a wider project with the Alan Turing Institute and the Department of Applied Mathematics and Theoretical Physics at Cambridge University to investigate molecular structure from images under physical constraints. In brief, the LMB position will focus on developing and implementing new machine-learning-driven algorithms within the RELION framework. The STFC position will focus on the data capture and training for these algorithms (as well as for the wider community), alongside application to molecular modelling. For full details and application please see: LMB position: https://mrc.tal.net/vx/lang-en-GB/mobile-0/appcentre-1/brand-3/xf-15f5592f8… STFC position: https://www.topcareer.jobs/Vacancy/irc255076_10934.aspx For those interested in both positions, we encourage you to apply for both. If you are unsure or would like further information please contact us. Best wishes, Tom and Sjors This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI.

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cctbx now available on conda-forge
by Billy Poon 23 Sep '20

23 Sep '20

Hi everyone, The conda-forge package for cctbx is now available. There are 2 packages, "cctbx-base" includes the base code and "cctbx" which includes "cctbx-base" and adds "wxPython", "PySide2", and "ipython". The commands for installing cctbx into your conda environment are conda install -c conda-forge cctbx or conda install -c conda-forge cctbx-base If you want to use Jupyter Lab, you can now easily do this with conda install -c conda-forge cctbx-base jupyterlab jupyter lab The existing documentation will be updated to reflect the easier installation procedure with conda. After installing the conda package, you can also run some of the tests (in an empty directory) with libtbx.run_tests_module module=libtbx module=cctbx nproc=<nproc> I do know of a few issues that I want to fix in upcoming releases, but please submit issues to https://github.com/cctbx/cctbx_project with steps to reproduce the error. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Issues with ligandfit.
by Vatsal Purohit 17 Sep '20

17 Sep '20

Hi, I’ve been using the Ligandfit function to location ligand binding sites using electron density obtained without any ligands in the structure model. However, recently, the program has been giving me the following error while trying to open the resolve maps: Sorry: None of the resolve versions worked Is there something I can do to try and fix this? Any advice would be appreciated. Regards, Vatsal Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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How to generate metal coordination restrain
by Shramana Chatterjee 17 Sep '20

17 Sep '20

Hi, I am trying to generate restraints for metal ions. Ready set is processing the pdb but it is not generating any output file. I don't want to add hydrogens to the model. Therefore readyset is generating only .edits file and finally I am unable to get any metal coordination restrains in Coot It would be very helpful if I get any suggestions about the above-mentioned problem. Thank you in advance. Regards, Shramana

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Job Vacancy: Postdoctoral research fellow position available in Therapeutics Discovery Division at MD Anderson Cancer Center
by Leonard,Paul G 15 Sep '20

15 Sep '20

Hi, A postdoctoral position is currently available in the Structural Chemistry group, part of the Institute for Applied Cancer Science (IACS) within the Therapeutics Discovery Division of MD Anderson Cancer Center. Our mission is to integrate novel biological insights with drug discovery expertise to accelerate the development of innovative, targeted, small-molecule therapeutics for unmet medical needs. Our work is conducted in a team science environment that brings together excellence in both academic and pharmaceutical discovery, as evidenced by recent publications. We are seeking a highly motivated individual with a strong background in structural biology, including protein expression and purification, protein crystallization, and X-ray crystallography structure determination. Experience with cryo-EM structure determination and/or structure determination of membrane proteins is not required, but would be advantageous. We are seeking only the most dedicated individuals who will join us in our quest to discover, develop and deliver more effective treatments to our patients. This is a unique opportunity to participate in project-driven drug discovery research within a highly respected academic and clinical setting. Interested individuals should apply via the Postdoc Jobs website. https://www.postdocjobs.com/posting/7069370 Paul Leonard Senior Institute Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Rebuild in place - Phenix AutoBuild
by Emad Alharbi 15 Sep '20

15 Sep '20

Dear Phenix developers, I have a question about using 'Rebuild in place' feature in Phenix AutoBuild. Which is recommended when you build MR case, set this feature to false or use the default option? I mean by saying default option to let Phenix AutoBuild decide. Thank you! ------------------------------ Emad Alharbi Research Student Department of Computer Science University of York,UK.

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Phenix and Coot v0.9
by Cygler, Miroslaw 14 Sep '20

14 Sep '20

Hi, I recently switched to Coot v0.9. When I start refinement now, the Coot starts and window opens but the model and density are not uploaded there and no phenix extensions show. I wonder is this is something that I can fix on my mac laptop or a bigger issue requiring work of phenix developers? Best, Mirek

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Improving Ramachandran plot
by Reza Khayat 09 Sep '20

09 Sep '20

Hi, I'm trying to follow the protocol described in White et al., Structural principles of SNARE complex recognition by the AAA+ protein NSF e-life 2018 https://elifesciences.org/articles/38888 Here is the pertinent paragraph: "To improve the Ramachandran statistics and geometry of the models, a two-parameter grid search of real space refinements was performed in which 3-5 macrocycles of global minimization and local grid search were performed in the presence of secondary structure restraints. First, a grid refinement search was performed for both target functions with around 1000 refinements each. For the emsley target function, rama_weight and scale_allowed were varied from 0.01 to 300; for the oldfield target function, a grid of refinements was performed over plot_cutoff values from 0.01 to 1.0 and weight_scale values from 0.1 to 300. Results were judged empirically and based primarily on a balance between CCmask and a minimal fraction of residues flagged by the program CaBLAM (Richardson et al., 2018<https://elifesciences.org/articles/38888#bib37>) because focusing on the fraction of residues with favored CCmask and Ramachandran statistics alone often resulted in unrealistic models with serious problems (Figure 12<https://elifesciences.org/articles/38888#fig12>, Table 2<https://elifesciences.org/articles/38888#table2>)." There are no differences in the refined structures regardless of what parameters I change. Attached is the input file I use for phenix.real_space_refine (1.18.2?). Altering the oldfield weight_scale (0.1 to 300) and plot_cutoff (0.1 to 0.5) makes no difference. Any help is highly appreciated. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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project directories
by Arthur Glasfeld 08 Sep '20

08 Sep '20

I’ve changed computers recently and for administrative reasons had to change my userID. As a result, all of the directories containing my phenix projects have changed. Is there a simple way to update the directories associated each project? Thanks Arthur ***************** Arthur Glasfeld Reed College Portland, OR 97202

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group on special position
by Arthur Glasfeld 04 Sep '20

04 Sep '20

I’ve run into a situation where I think I have a phosphate sitting on a 3-fold axis, where the P to O1 bond lies on the axis and the atoms O2, O3 and O4 are in symmetry-related positions. The data go to 1.6 Å, so it looks pretty convincing. I’m refining this in Phenix and have tried some tricks with occupancy - fixing the atoms at 0.33, but I get a lot of positive density in the Fo-Fc map and large B-factors. I’ve looked around but am not finding ideas on how to model this correctly in my structure file - the references I find are for monoatomic ions. Any advice would be welcome. Thanks, Arthur ***************** Arthur Glasfeld Reed College Portland, OR 97202 Office: (503)517-7679

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