- phenixbb - phenix-online.org

Mask used for map-to-model FSC
by Yang Shi 19 Oct '20

19 Oct '20

Hi all, Does anyone happen to know how to control the tightness of a mask for map-to-model FSC calculation? I have tried the "atom radius" in Map/Model CC tab of "Comprehensive validation (cryo-EM)", but it was not working for me. The reason I am asking this question is that I can only model a small region in the cryoEM map, the rest is unknown to me. Then the CC in low-frequency was 0.4-0.6 in the FSC curve, while the overall masked cc was 0.85. I would like to find an easy way to make the FSC curve look better. Any suggestions would be appreciated! Best wishes, Yang

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Opening Coot through Phenix in Window
by Thomas, Leonard M. 14 Oct '20

14 Oct '20

Hello, Most likely a simple problem, I am helping a some of our students setup their computers to use Phenix and Coot for both their own work and a class. One has installed both Phenix and Coot but cannot get Phenix to open Coot and display the model or maps on a Windows box, Coot is opening just not displaying. I admit I don’t work with Windows that often and I am not sure what the problem could be. Thank you in advance for any insight. Cheers, Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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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 08 Oct '20

08 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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How to generate metal coordination restrain
by Shramana Chatterjee 16 Sep '20

16 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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General interest re research data
by John R Helliwell 01 Sep '20

01 Sep '20

Dear Colleagues, A couple of research data matters that I imagine will be of general interest I have placed at the IUCr CommDat Forum:- The Photon and Neutron EU Facilities Open Science Cloud announced their “doi per experiment” described in this 3 minutes youtube movie clip https://forums.iucr.org/viewtopic.php?f=39&t=431 Secondly, the Swiss Universities Bulletin have produced a special issue on Research Data Management, to which I have contributed an article on Open science and the reproducibility of the scientific record https://forums.iucr.org/viewtopic.php?f=39&t=432 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

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Phenix User Workshop, 15th and 16th of September
by Paul Adams 31 Aug '20

31 Aug '20

Dear Colleagues, The Phenix developers will be holding an online Phenix User Workshop on the 15th and 16th of September at 8am-12pm PDT. These times will work best for researchers in North and South America, Europe and Africa. We plan to hold a future workshop at a time better suited to researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of crystallography and cryo-EM in Phenix, with the final emphasis based on the applicants’ research interests. To apply, send email to workshops(a)phenix-online.org with a short paragraph about your interests. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. Cheers, The Phenix Developer Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) 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) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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phenix.resolve_cryo_em
by Reza Khayat 25 Aug '20

25 Aug '20

?Hi, I'm running into a clipping issue with phenix.resolve_cryo_em. The program seems to be improving the map; however, portions of the map get clipped. Any suggestion would be 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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MicroED Imaging Center
by Johan Hattne 24 Aug '20

24 Aug '20

Dear Structural biology community; We are delighted to announce that the National Institutes of Health is helping us establish a Biotechnology Development Research Center focused on MicroED at UCLA School of Medicine, named MicroED Imaging Center (MEDIC). The main thrust of MEDIC is for method development and research focused on MicroED. As part of community engagement, the center will host the annual MicroED course as well as an annual MicroED Summit, both of which will be staged at the UCLA School of Medicine, and open to the community on a first come first serve basis until spaces are filled. Approximately 90% of available spots will be allocated to academic attendees and 10% to industry attendees. This will be a continuation of almost 10 years of tradition of providing workshops and training to the community. Also, there is some opportunity for the community to collect data on MEDIC microscopes. There is also limited availability for one-on-one user training at the center at UCLA for microscope set up and data collection. Users and trainees will be invited based on replies to a call for proposals, which will be advertised shortly. The proposals will be reviewed by an advisory committee. Because of the COVID19 pandemic and the limitations on travel and hosting imposed by UCLA we cannot begin these activities at this stage. On a related note, UCLA School of Medicine is also running a MicroED Imaging Core which is open as a pay per use service for academia and industry. This activity is independent of the Gonen Lab and from the NIH funded research program on MicroED. Details can be found online. Kind regards Tamir Gonen and Pawel Penczek

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error while Auto sharpen
by sangeeta niranjan 19 Aug '20

19 Aug '20

Hello, I am trying to use Auto Sharpen feature of a CyoEM refined map into Phenix but the job is getting failed every time with the following error: Missing the model file: followed with model file name and location. Although it was working before but now it's showing the same error for all the auto sharpen runs including Models/PDBs. Thank you -- Sangeeta Niranjan Ph.D. Student, Lab of structural Biology Lab-6 NB National Centre for cell Science Ganeshkhind, Pune, India

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moving folders
by Thomas, Leonard M. 18 Aug '20

18 Aug '20

Hello, I know this come up every so often by my google-fu is sorely lacking to find the answer. How does one move a project folder? I have a project and not thinking things through set it up in the wrong folder. I would like to move the whole thing to another folder maintaining the project structure. Thanks, Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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