- phenixbb - phenix-online.org

phenix.resolve_cryo_em resolution and real space refinement
by David Lawson (JIC) 14 Oct '20

14 Oct '20

Hi All, I have run phenix.resolve_cryo_em using half maps at 7.5 A resolution (the postprocessed map is at 7.1 A) and I just wanted to clarify a couple of things (I have pasted the end of the logfile below this message). I set the resolution to 7.52 A but didn't supply a resolution for density modification - it seems to have chosen a value of 5.671 A (1) It states "Estimated improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A" suggesting to me that it agrees with the postprocessed resolution. Is this the value of 7.08 on this line: "FSCref=0.5: 7.08 6.69 6.63"? (2) I understand that the actual process of real space refinement doesn't care about the resolution of the map, but you need to supply it to get meaningful CC values. So my question is what resolution should I supply to RSR if I use the density modified map? I realise that a value of "-0.450 A" is at the upper end of what to expect from density improvement, but I can report that the DM map does look noticeably better than the postprocessed map, especially in regions that are less well defined. Many thanks in advance for any advice Dave Lawson ----------------------------------- d-values (A) where FSCref=0.5: 7.08 6.69 6.63 Estimated improvement in d_cc_star=0.5: -0.450 A This is new current best working_map_coeffs_info. Estimated improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A Done testing....R-value: 0.530 Try: 1 ['database 5', 'resolution: 5.67 ', 'dm_resolution: 5.67 ', 'density_modify_unsharpened_maps:False', 'apply_cc_star:True', 'b_iso: None A**2'] Best density modification cycle 1 is try 1 with Methods used: ['database 5', 'resolution: 5.67 ', 'dm_resolution: 5.67 ', 'density_modify_unsharpened_maps:False', 'apply_cc_star:True', 'b_iso: None A**2'] R-value: 0.530 Estimated improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A Result: -0.450 A to d_min(FSCref=0.5): 6.628 A R-value: 0.530 Wrote working map to /home/lawsond/phenix/ResolveCryoEM_1/map_denmod.ccp4 =============================================================================== SUMMARY AFTER CYCLE OF DENSITY-MODIFICATION =============================================================================== Overall best density modification Cycle 1 try 1 Estimated improvement: -0.450 A to d_min(FSCref=0.5): 6.628 A R-value: 0.530 Denmod resolution: 5.671 A Database: 5.000 A Writing out final map files... ------------------------------- Prof. David M. Lawson Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.lawson(a)jic.ac.uk

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Quest for resolution-sensitive substructure determination cases
by Randy Read 11 Oct '20

11 Oct '20

Dear members of the BBs, When determining the anomalous substructure as part of SAD phasing, one of the most important parameters can be the choice of resolution limit for the data provided to the substructure determination algorithm. Extending to too high resolution can hamper the search by introducing too much noise. The resolution limit is varied internally in phenix.hyss, but is provided as a parameter to SHELXD. There are various rules of thumb that people use to make a first choice of resolution limit, such as half-dataset anomalous correlation or the average precision of the anomalous differences, or even just adding 0.5 to dmin. We’re currently exploring some alternative measures and we would like to test them on a significant number of relevant test cases. It turns out that a large proportion of SAD data deposited in the PDB have such good signal-to-noise that substructure determination succeeds with a wide variety of parameters, so we’ve only collected a few cases so far. It would be great if you could let us know of cases that you’re aware of, where substructure determination succeeds with the right choice of resolution limit but fails with the full resolution range of data. Of course, these have to be cases where the diffraction data have been deposited at the PDB or otherwise been made available. We prefer data for which the intensities, and not just the amplitudes, are available, but we won’t be too picky if that would limit the number of examples too much! If you email me directly, I’ll post a summary to the BBs. Thanks! Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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questions regarding phenix.table_one
by Wei Wang 09 Oct '20

09 Oct '20

Dear all, I’m using phenix.table_one to prepare the statistics to include in the paper, and came up with a question regarding the number of reflections being reported. For example, one of the structures has the following statistics: Unique reflections: 70764 (7064) Reflections used in refinement: 70731 (7019) Reflections used for Rfree : 3523 (371) Clearly 70731+3523 is greater than 70764. So I’m puzzled here. I guess “Reflections used in refinement” number actually equals to the sum of "Reflections used for Rfree”+”Reflections used for Rwork”. If this is true then I would just do a simple calculation myself to get the ”Reflections used for Rwork”. Another question is I’m seeing “Reflections used in refinement” always a little smaller than “Unique reflections”. I guess it’s because there’s an outlier rejection in certain step but not sure. I’d be grateful for any clarification. thanks ! Regards, Wei

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phenix.refine read .geo file
by Sheila Boreiko 08 Oct '20

08 Oct '20

Dear all, For the sake of some experiment, I would like to manually edit some restraints of a geometry restraint file (normally named .geo) and ask for phenix.refine to read this edited file rather than producing a new one, is this possible? What should be the command line to read this geometry restraint file be? Thank you, Sheila

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Tenure track faculty position University of Missouri
by Tanner, John J. 07 Oct '20

07 Oct '20

Dear Colleagues, My department has begun a search for a tenure track faculty position. Structural biology is among the preferred areas of biochemistry for this search. More information in available here: https://biochem.missouri.edu/open-positions/ Review of applications will begin on November 16, 2020. John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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Newcastle University Professor/Reader/Senior Lecturer of Structural Biology
by Arnaud Basle 05 Oct '20

05 Oct '20

Dear All, Newcastle University is delighted tobe recruiting for a Professor / Reader / Senior Lecturer of Structural Biology to work within the Biosciences Institute in the Faculty of Medical Sciences. https://jobs.ncl.ac.uk/job/Newcastle-ProfessorReaderSenior-Lecturer-of-Stru… Cheers, Arnaud -- Dr Arnaud Basle X-ray facilities manager Newcastle Structural Biology Laboratory Biosciences Institute Faculty of Medical Sciences Newcastle University Framlington place NE2 4HH Newcastle upon tyne Phone 0191 208 5482

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Scientist-I (Structural Biology) position at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 05 Oct '20

05 Oct '20

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist-I with experience in protein chemistry and structural biology. The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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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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