- phenixbb - phenix-online.org

Fw: on phenix.real_space_refine
by Smith Lee 19 Oct '15

19 Oct '15

Dear Pavel, On Oct 9, 2015 I have e-mailed to you my experience with 1.9-1692 and version 1.10 (and 1.10.1) on phenix.real_space_refine. Today I just completed another protein phenix.real_space_refine. For the following comparison runs, the initial model same, the map same, all 5 macro_cycles default run. For version 1.10.1, the results were as following, Map CC (whole unit cell)： 0.672Map CC （around atoms）： 0.761rmsd （bonds): 0.01rmsd (angles): 1.55All-atom clahscore: 39.27Ramachandran outlier: 0.98%Ramachandran allowed: 12.71%Ramachandran favoured: 86.31%Rotamer outliers: 0.91%C-beta deviations: 0 For version 1.9-1692, the results were as following, Map CC (whole unit cell)： 0.645Map CC （around atoms）： 0.687rmsd （bonds): 0.0071rmsd (angles): 1.15All-atom clahscore:16.88Ramachandran outlier: 2.00%Ramachandran allowed: 6.23%Ramachandran favoured: 91.77%Rotamer outliers: 0.05%C-beta deviations: 0 For the version 1.10.1 phenix.real_space_refine, the most unacceptable was on the clashscore, the whole refine process seems did not care on the clashcore refine at all. I am looking forward to getting an explanation from you on the causes of the difference for phenix.real_space_refine for the 2 versions, and the possible strategy we can take to eliminate the difference to get the acceptable results. Best regards. Smith On Friday, October 9, 2015 12:52 AM, Smith Lee <smith_lee123(a)yahoo.com> wrote: Dear Pavel， As I have told you, I have tried phenix.real_space_refine for 2 protein with version 1.9-1692 and version 1.10 (and 1.10.1) for many times, with cif or without cif, with or without annealing. The general feedback was that the version 1.9-1692 was much much better for the final analysis of the PDB given at the end of the run of the phenix.real_space_refine. Especially for clashing score, version 1.9-1692 can gave acceptable results (below 20 or around 20), but the clashing score given by the above 2 new versions of phenix.real_space_refine was very high (around 50 or 100). For C-beta deviations, the output by 1.9-1692 was also much better Before I have tried the other nightly built versions of phenix.real_space_ refine between version 1.9-1692 and version 1.10 (and 1.10.1) , all I gave acceptable output analysis (something like the Molprobity analysis at the end of the run). Thus may I ask the reason you have version 1.10 (and 1.10.1) phenix.real_space_refine was because you have realized that the result given by version 1.9-1692 was too satisfactory? One direct concern of me was that you have recommended not to use the old version phenix. But I cannot get the satisfactory result with the new version phenix.real_space_refine. The other concern of me was that, I have noticed there were publications In Nature and Science which wrote they use phenix.real_space_refine to got the results in Nature and Science. The Phenix they used should be the versions earlier than version 1.10. Considering what I mentioned above, the Nature and Science results may be not so correct, if new version of phenix was considered as much better than the old version. Thus am I the only user who communicated with you on the high clashing score given by the new version of phenix？Can you give some comments on what I mentioned above on the high clashing score given by the new version phenix.real_spac_refine? Best regards. Smith

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Visualise NCS operators
by Morris, Kyle 17 Oct '15

17 Oct '15

Dear Phenix community, After running $ phenix.find_ncs what would be the best way to visualise the operators found and detailed in the *.ncs_spec file superimposed on the map used in the search? Thanks for your help! Best wishes, Kyle

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Postdoctoral Position in Structural Biology at ICR, London, UK
by Sebastian Guettler 16 Oct '15

16 Oct '15

Dear PHENIX Community, Please see below for details of a postdoctoral position in our team. Best wishes, Sebastian Guettler Postdoctoral Position in Protein Biochemistry / Structural Biology / Electron Microscopy We seek to appoint a Postdoctoral Training Fellow to the research team led by Dr Sebastian Guettler in the Divisions of Structural and Cancer Biology at The Institute of Cancer Research in London, UK. The position is funded by Cancer Research UK. The successful applicant will undertake biochemical, structural and functional studies on members of the ADP-ribosyltransferase (or “PARP”) family of proteins and macromolecular complexes containing PARPs. Our goal is to gain insight into the control and cellular roles of these enzymes with a specific interest in ADP-ribosyltransferase-dependent signalling processes linked to cancer. Applicants should possess a PhD in a biological science such as biochemistry or molecular biology. Experience with recombinant DNA techniques, high-quality protein expression and purification, protein characterisation, structural biology, as well as some experience in structural electron microscopy are essential. Appointment will be on a Fixed Term Contract for 3 years in the first instance. The full salary scale is in the range from £29,517 to £42,187 p.a. inclusive. Starting salary will be based on previous postdoctoral experience. To apply, please submit your CV and covering letter online. Please include the names and addresses of two referees. For further details and instructions on how to apply, please refer to our online vacancy and recruitment site at http://www.icr.ac.uk/jobsearch, quoting job reference number 1494999 for this position. While applications need to be placed via our online system, informal inquiries can be sent to Dr Sebastian Guettler at sebastian.guettler(a)icr.ac.uk<mailto:[email protected]>. Please do not submit your formal application by email! Summary: Closing Date of vacancy: 31 Oct 2015 Type of Contract: Fixed Term, Postdoctoral Training Fellow Length of Contract: 3 years Salary Range: £29,517 p.a - £42,187 p.a. inclusive (full salary scale) Work Location: London Research in the Divisions of Structural and Cancer Biology focuses on the functional, biochemical, and structural characterisation of cellular processes relevant to cancer and cancer therapy. The Division of Structural Biology has managed state-of-the-art facilities for protein crystallography (crystallisation robots, Bruker Microstar and CCD detector), cryo-electron microscopy (FEI Tecnai F20 and T12), and protein production with expertise in multi-subunit expression (insect cell, yeast and bacterial expression, including a 60-litre fermentor). The Division is also well-equipped with instrumentation for biophysical analysis (e.g. ITC, fluorescence, multi-angle light scattering). The Division of Cancer Biology provides a state-of-the-art infrastructure for mammalian cell culture, imaging, mammalian genetics, chemical biology and proteomics. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Local B-factor for a ligand
by Karchevskaya, Anastasia 16 Oct '15

16 Oct '15

Dear Phenix users, Can you, please, clarify, how can I get local B factor for the residues around the ligand. 1) I saw this reply in an archive: http://www.phenix-online.org/pipermail/phenixbb/2011-March/016819.html 2) But it doesn't suit me, because, for instance in this case: http://www.rcsb.org/pdb/explore/explore.do?structureId=4RUP the interacting residues are: http://www.rcsb.org/pdb/images/H97:4RUP_psv_v_500.png 302, 265, 175, 423 can be fitted into a sequence, but I don't need everything in between them 3) There is also another option: http://www.ebi.ac.uk/thornton-srv/databases/PDBsum/ru/4rup/grow.out I can extract interactions from here and make a request to Phenix. If so, can I request the b-factor just for one exact amino acid? Thank you in advance, Anastasia

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peaks and holes for a difference map
by Murpholino Peligro 15 Oct '15

15 Oct '15

Hi. Is there a way to load a pdb and a difference map (ccp4 format) in phenix, command line is better, and then get something like the "validate->difference map peak" analysis (as in coot)..? Thanks

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MRC map as molecular replacement model
by Acharya, Priyamvada (NIH/VRC) [C] 15 Oct '15

15 Oct '15

Hi all, I want to use an MRC map obtained by low resolution EM reconstruction, as molecular replacement model in Phaser. I serached the phenixbb archives and learned that I should us phenix.map_to_structure_factors to convert the map file to mtz so it can be input into Phaser. When I do that I get an error "Sorry: Map must have origin at (0,0,0): recenter the map and try again". I have two questions? 1) What tool should I use to recenter the map and 2) Is there a better way to do this? Thanks in advance for your replies. Best regards, Priyamvada

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2016 MicroED workshop at Janelia Research Campus (Reminder)
by Hattne, Johan 15 Oct '15

15 Oct '15

Reminder: the deadline for applications for the workshop is this Sunday, October 18. The original announcement (minus a few typos) is included below. Janelia Research Campus (Ashburn, VA) will run a MicroED workshop February 22-25, 2016, hosted by Tamir Gonen. MicroED is a technique that uses electron diffraction to facilitate structure determination from sub-micron sized crystals, eliminating the need to grow large crystals. MicroED uses equipment and procedures that are standard on many cryo-TEM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To encourage the widespread use of MicroED we are offering this workshop to teach microscopists how to perform the technique and adopt it at their own institutions. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Space in the course is limited. Those interested should send a brief statement on why they wish to participate to conference(a)janelia.hhmi.org by Sunday, October 18. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

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Announcing the 2015/2016 EMDataBank Model Challenge
by Cathy Lawson 15 Oct '15

15 Oct '15

Dear PhenixBB List Members, EMDataBank is pleased to announce the 2015/2016 Model Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Benchmark targets of varying size and complexity have been selected from recently deposited 3DEM structures based on current state-of-the-art detectors and processing methods, in the resolution range 2.2-4.5 Å. Challengers are sought to create and validate models from challenge target maps in four different categories (1. optimize current cryoEM model, 2. fit known related cryoEM, crystallographic, or comparative models, 3. ab initio model building, 4. any other method of map interpretation), and upload their results with associated details. Assessors are sought to participate in evaluating submitted models. Registration is now open for all interested participants. Challengers may submit their models between November and April. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in late 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MODEL CHALLENGE" in the menu bar. This is the second of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. The first challenge is focused on creating reconstructions from raw 2D image data and is currently in progress (click on "MAP CHALLENGE" in the menu bar). Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Model Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

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Question regarding uploading 2Fo-Fc map into KiNG
by Natalia Ketaren 07 Oct '15

07 Oct '15

Hello All, I have a question regarding the KiNG program: I used MolProbity to assess the quality of my model which revealed some poorly fitted residues in my structure. I want to correct these residues using KiNG but am having problems uploading the electron density map. Does the program not accept .mtz maps generated by coot? Do I have to convert the map into another file format? If so, would you be able to suggest a program for me with which to do this? Any help would be greatly appreciated! Kind regards, Natalia _____________________________ Natalia E. Ketaren, PhD Postdoctoral Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

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Phenix bug fix version 1.10.1 released
by Paul Adams 07 Oct '15

07 Oct '15

A bug fix version of Phenix is now available (build 1.10.1-2155). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ This addresses the following issues: - Incorrect location used for heavy atom files when running AutoBuild in certain circumstances - Errors when adding hydrogens to waters in ReadySet - Errors when using GUI helper applications that handle sequences (e.g. Blast search) Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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