- phenixbb - phenix-online.org

problem phenix ensemble
by Firas FADEL 25 Feb '14

25 Feb '14

Hello, I am using phenix ensemble to refine an X-ray structure of a protein (40kDa) at 1.05 A in complex with a ligand. The occupancy of the ligand is 73%. After refining the structure, I found out that the program confused the position of the ligand and put some water molecules. Do you have any suggestion or a command to avoid this problem. If you need details I can send you the mtz and pdb files. Thanks in advance. Firas Fadel Firas FADEL Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC Equipe Alberto PODJARNY, 1 Rue Laurent Fries, 67404 Illkirch-France Email : fadel(a)igbmc.fr<mailto:[email protected]> Tel: + 33 (0) 3 88 65 33 13<tel:%2B%2033%20%280%29%203%2088%2065%2033%2013>

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Announcement: QuantumBio Release of QM-based X-ray Crystallography Plugin v1.0 for Phenix
by Lance Westerhoff 25 Feb '14

25 Feb '14

Hello All- We are pleased to announce the release of our linear scaling, quantum mechanics DivCon Discovery Suite plug-in v1.0 for the Phenix, x-ray crystallography platform. As was detailed in the recent Phenix Newsletter, when this plugin is installed, the conventional refinement functional along with the stereochemical restraints or CIFile for the ligand(s) and for the surrounding active site(s) are replaced with QM data in "real time" during the refinement in order to increase structural accuracy and decrease artificial strain. To see the full press release along with references and links for further information, please take a look at the following website: http://www.quantumbioinc.com/news/show/PhenixAnnouncement To encourage adoption, we have waived the license fee for non-profit, academic use and we have posted our commercial evaluation license as well. These licenses are available at the following link: http://www.quantumbioinc.com/products/software_licensing Certainly, let me know if you have any questions or if you would like to try out the technology on your own structures. -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com

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revisiting "Problem with loop fitting "
by Alejandro Buschiazzo 24 Feb '14

24 Feb '14

Dear phenix community I am attempting to use phenix.fit_loops for the first time and getting an error message: "No suitable gap found matching residues" I found a short exchange exactly about this (Jan 2011), but eventually Tom Terwilliger asked for the files directly to see if he could solve it. I can't seem to find a later summary of the solution. (apparently, the most probable reason was some kind of mismatch between PDB numbering and sequence file...which I shouldn't have... I'm probably missing some silly here - I have been fiddling around with the sequence file in many ways...with no success) many thanks for any help! alejandro -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Questions about phenix.mr_rosseta
by Yonglin Hu 24 Feb '14

24 Feb '14

Hello List, I am very new to using Phenix/Rosetta to solve MR. I just finished a job by following the procedures described on phenix-online.org using Phenix GUI. The program reported that no solution was found, but when I went through the RUN_FILE_*.log, I found that despite all the log files ended with the following sentences: Stage to relax: refined_rescored_rosetta_solution No solutions to relax No autobuilt solutions to iterate... Finishing up mr_rosetta... one solution had a Rfree of 0.48 with correct number of molecules in ASU. When I refined that solution using phenix, Rfree went down further, proving to be a correct one. So my question is: why phenix.mr_rosetta did not report this solution as a good one? My second question is regarding model rebuild using phenix/rosetta. No matter I used the GUI or command lines copied from phenix-online like the following: phenix.mr_rosetta \ seq_file=~/MA/Mpa.pir \ data=~/MA/MA.mtz \ search_models=~/MA/refine_6.pdb \ already_placed=True \ fragment_files = ~/MA/MA-3mer \ fragment_files = ~/MA/MA-9mer \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=6 \ space_group="C 1 2 1" \ use_all_plausible_sg=False \ nproc=4 the program always fails. The log files have the following messages: Sorry, a subprocess has failed... ...... Sorry: Failed to run REBUILD...see log file in MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log They pointed to rebuild.log files, but these files don't contain error message and they ended with the following seemingly innocuous lines: protocols.relax.FastRelax: CMD: accept_to_best -3682.86 0.994359 0.994359 0.44 core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 requested but only 401 protein CA atoms found. core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 requested but only 401 protein CA atoms found. protocols.relax.FastRelax: CMD: endrepeat -3682.86 0.994359 0.994359 0.44 protocols::checkpoint: Deleting checkpoints of FastRelax protocols::checkpoint: Deleting checkpoints of FastRelax protocols.jd2.JobDistributor: S_MA_R_0005 reported success in 4573 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 5 jobs considered, 5 jobs attempted in 20716 seconds I would appreciate it if you could tell me what could be the causes of the failures. Thank in advance, Yonglin

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stop_for_unknowns=False in new version ?
by Michaela Renner-Schneck 19 Feb '14

19 Feb '14

Hi, I haven’t been running phenix.refine for a couple of weeks and meanwhile we have updated to the latest version. Now I need to re-run an old job but unfortunately the pdb-interpretation option "stop_for_unknowns=False“ which I needed for this seems to be no longer valid. Is there a way to get this option work again ? thx in advance Michaela

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New position
by Gillette, William (NIH/NCI) [C] 19 Feb '14

19 Feb '14

Dear colleagues, We have an opening for a structural biologist here in Frederick, MD. If not interested, please forward this email to those who might be. Thank you. Best regards, Bill <http://jobs.leidos.com/job/Frederick-Lead-Structural-Biology-603181-%28NCI%…> http://jobs.leidos.com/job/Frederick-Lead-Structural-Biology-603181-%28NCI%… ______________________________________________________ Bill Gillette, Ph.D. (Contractor) Sr. Scientist, Protein Expression Laboratory Cancer Research Technology Program Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research (FNL) P.O. Box B, Frederick, MD 21702 Phone: 301-846-1029 William.Gillette(a)nih.gov<gillettew(a)mail.nih.gov> Notice: This communication may contain privileged or other confidential information. If you are not the intended recipient, or believe that you have received this communication in error, please do not print, copy, retransmit, disseminate or otherwise use the information. Please indicate to the sender that you have received this email in error and delete the copy you received.

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phenix.composite-omit-map and PBScluster
by Mark A Saper 19 Feb '14

19 Feb '14

Hi, This is a technical question for cluster experts. I tried to run phenix.composite-omit-map which can divide the calculations into separate jobs, on a very large cluster controlled by the PBS system. I used this command of which the first 2 lines specify to divide the work up into 16 processes, and each process will use 1 of the CPU's in the cluster. phenix.composite_omit_map nproc=16 background=False technology=pbs \ qsub_command="qsub -V -l procs=1,walltime=00:30:00,mem=2000mb,qos=flux -j oe -M saper(a)umich.edu -q flux -m abe " \ omit_type=anneal map_type=2mFo-Dfc output.file_name=composite_omit_map9.mtz \ reflections3_5percent.mtz Refine_122.pdb This is the end of the log file before it aborted: ----------Calculating individual omit maps---------- |-----------------------------------------------------------------------------| | target_work(ml) = 4.65539 r_work = 0.1750 r_free = 0.2066 | |-----------------------------------------------------------------------------| And this is the error log: Traceback (most recent call last): File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 238, in <module> run(sys.argv[1:]) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 166, in run out=out) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/phenix/phenix/automation/composite_omit_map.py", line 395, in __init__ preserve_exception_message=True) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/easy_mp.py", line 502, in parallel_map display_stderr = not preserve_exception_message, File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/queuing_system_utils/processing/__init__.py", line 405, in PBS raise RuntimeError, "PBS does not support synchronous submission" RuntimeError: PBS does not support synchronous submission I know that PBS doesn't support synchronous submission. Perhaps each job (or map region) requires more than one processor? Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan c/o Biophysics, Chem 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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list policy change: Reply-To header
by Nathaniel Echols 18 Feb '14

18 Feb '14

Hi all-- Since the current practice of directing all replies to the entire phenixbb seems to cause confusion, we've changed this so the reply will be sent to the original sender. Because we rely on the list archives as a form of ongoing "live" documentation, we encourage everyone to use "reply to all" unless you are really certain that you do not want your message to go to the list. (This especially applies to my colleagues: if you don't copy the entire list, the rest of us have no way of knowing if a question has been answered or not.) thanks, Nat

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Re: [phenixbb] Real space refinement
by Pavel Afonine 18 Feb '14

18 Feb '14

Hi Mavis, there are two options. One is convert your EM map into structure factors Fobs and HL coefficients using phenix.map_to_structure_factors command and then use phenix.refine to do reciprocal space refinement. This is somewhat indirect way. The good thing about it is that phenix.refine has a broad range of tools to handle low resolution refinement. Another option is to use phenix.real_space_refine to refine model against the map directly. This is a preferred way but phenix.real_space_refine is new, less mature program and it generally is still under development (though it's functional if you try it now). So if it does not work as you expected or you have any feature requests or any questions or any other feedback - please do not hesitate to let me know, as this may help to improve this tool. All the best, Pavel On 2/17/14, 6:14 AM, Agbandje-Mckenna,Mavis wrote: > Dear Pavel, > > Thank you so much for getting back to me - this is much appreciated. We received a script from Hong Zhou's group who have been using Phenix to refine the model for their 3.3 Angs cryo-EM Aquareovirus structure that we were going to try but this seems a lot more simpler! > > Thanks again. I will let you know how it turns out. > > And thank you for the attached pdf. > > Best wishes > > Mavis > > Mavis Agbandje-McKenna, Ph.D. > Director, Center for Structural Biology > Professor, Dept. of Biochemistry and Molecular Biology > Center for Structural Biology > The McKnight Brain Institute > P.O. Box 100245 Tel.: 1-352-392-5694 > University of Florida Fax.: 1-352-392-3422 > Gainesville, FL 32610-0245 e-mail: mckenna(a)ufl.edu > Website: http://msg.mbi.ufl.edu > ________________________________________ > From: Pavel Afonine [pafonine(a)lbl.gov] > Sent: Monday, February 17, 2014 2:28 AM > To: Agbandje-Mckenna,Mavis; phenixbb(a)phenix-online.org > Cc: Lins, Bridget; Drouin,Lauren M > Subject: Re: Real space refinement > > Hi Mavis, > > you can do it in Phenix. Command line tool for this is: > phenix.real_space_refine. Just give it map and model and see what > happens, like this: > > phenix.real_space_refine model.pdb ccp4_formatted_map.map > > I wrote this program specifically to do various kinds of model > refinement against the map, with the main focus on EM maps. Have a look > at the article that briefly describes it here: > http://www.phenix-online.org/newsletter/CCN_2013_07.pdf > "New tool: phenix.real_space_refine". > The article is from last year but I haven't done much since then so it > pretty much documents the current state of the art. > > Should you have any questions or problems or need any help with this > please let me know off list. > > All the best, > Pavel > > On 2/14/14, 8:45 AM, Agbandje-Mckenna,Mavis wrote: >> Dear Pavel, >> >> I don't believe we have met, but you have received several e-mails from people in my group (including Sujata (Tina) Halder) and also helped them with their use of Phenix - thank you. >> >> I have a question for you regarding real space refinement in Phenix. We have a 3.7 Angs cryo-EM reconstructed structure for a virus capsid and we have been able to build a model for the capsid VP using COOT. I would like to refine this model further against the map using real space refinement. I am trying to find a suitable program that would allow me to do this. I believe Phenix can do it, but I am not sure. Could you give me some direction? >> >> Thanks in advance. >> >> Best wishes >> >> Mavis >> >> Mavis Agbandje-McKenna, Ph.D. >> Director, Center for Structural Biology >> Professor, Dept. of Biochemistry and Molecular Biology >> Center for Structural Biology >> The McKnight Brain Institute >> P.O. Box 100245 Tel.: 1-352-392-5694 >> University of Florida Fax.: 1-352-392-3422 >> Gainesville, FL 32610-0245 e-mail: mckenna(a)ufl.edu >> Website: http://msg.mbi.ufl.edu

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Gordon Conference on Diffraction Methods in Structural Biology
by Anastassis Perrakis 17 Feb '14

17 Feb '14

Dear all, The biannual Gordon Research Conference in Structural Biology, accompanied by the first Gordon Research Seminar, will take place in the last week of July at Bates College, New England, a few hours drive from the IUCr meeting that follows in the first week of August. The theme for the GRC is "Faster, Smaller, Better: Novel Technologies for Diffraction Experiments in Molecular Biology and Drug Discovery" and of the GRS (which precedes the GRC and is targeting young scientists giving them an opportunity to present their own work to their peers prior to the meeting) "Towards Integrative Structural Biology". We have a truly fantastic line of speakers and discussion leaders, including John Kuriyan , Randy Read, Ana Gonzales, Ilme Schlichting , Henry Chapman , John Spence, Graeme Winter , Aina Cohen, Thomas Schneider , Gwyndaf Evans , Bob Fischetti , Flora Meilleur, Janet Newman , John Hunt , Michael Duszenko , Jose Antonio Marquez, Paul Adams , Clemens Vonrhein , Airlie McCoy , Brent Nannenga, Zbyszek Dauter , Tom Terwilliger , Garib Murshudov , Gerard Kleywegt , Paul Emsley, Dmitri Svergun , Peter Zwart , Michael Hammel , Lois Pollack, Elspeth Garman, Lisa Keefe , Gary Gililland , Aydnan Achour and Giovanna Scapin. For more details visit our web site: https://www.grc.org/programs.aspx?year=2014&program=diffrac And here is the largely unavoidable motivational speech for anyone interested to my highly biased personal view: I first went to this meeting in 1998, as a young post-doc, presenting results that later led to the 'ARP/wARP' software: in fact, I had changed my slides (for the younger audience: slides were pieces of photographic film that were typically projected as mirror images of what you really wanted) a month or so before the meeting, as we got our very first models auto-built. I thought it was the most educational and exciting meeting I have ever been to, and in many ways it has shaped my research plan and my career (and my hate for golf). I wish I could also say that I never missed any of the subsequent meetings, but courtesy of the US Visa authorities and the Greek Army, I actually did a miss a couple. However, I still find them as exciting as so many years ago, but for a whole different set of scientific reasons: the diffraction methods landscape is changing rapidly, new machines and concepts make possible experiments that we do not even know what they are going to be! I am honored to be chairing this year's edition, and I hope that I will hear from at least one of you, what I had heard from a few before: "this is the best meeting I have been in my life". Science aside, I am glad there is no golf course nearby the Bates College site where we are holding this meeting for the last decade, I am equally happy for the "Great Outdoors" site where we do the mid-week excursion, and I am looking forwards to the football (sorry: "soccer") and basketball games. The Bates College boasts an excellent auditorium for the talks, a truly outstanding lounge for the poster sessions (that are always accompanied by drinks, an observation that might partially explain the tendency to finish well after midnight in a very positive spirit) and a somewhat confusingly and an unexpectedly good quality restaurant in the very friendly College site. A limited amount of (partial) bursaries to young scientists will be available for this year - when this becomes definitive we will post the news. I should also mention that one session will host eight seminars that will be selected from the poster sessions, giving all particpants the opportunity to present their own research! In the meantime, I am looking forward to welcome you all at the meeting and I hope you will register ... today! Best regards, Tassos Anastassis (Tassos, Perrakis, Principal Investigator , Staff Member Department of Biochemistry (B8, Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile , SMS: +31 6 28 597791

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