- phenixbb - phenix-online.org

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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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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