April 2015 - phenixbb - phenix-online.org

Autobuild on parallel
by Kaushik Hatti 29 Apr '15

29 Apr '15

Hi, What is the best way to run Autobuild if I need to run it on hundreds of datasets (through command-line)? I have a single machine with 24 cores and access to a cluster with 128 cores (on parallel; accessible only through PBS script). Each Autobuild job with nproc=4 on a single core machine takes ~12 hours to run (nproc > 4 wouldn't make any difference in the speed of computation?!). However, I read that I could set nproc=10 (or more) and run on parallel ( https://www.phenix-online.org/documentation/reference/autobuild.html#parall…). When I tried the same through PBS script, I got the following error, XXXXXXXXXXXXXX Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running with 1 processors using qsub background=False nproc=20 background=False in ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1.log Traceback (most recent call last): File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 2364, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 4647, in AutoBuild_rebuild_cycle_run always_reuse_model=always_reuse_model) File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7452, in AutoBuild_build_refine mtz_file=mtz_file,mtz_ref_file=mtz_ref_file) File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7696, in run_standard_build_in_parallel r.run(out=sys.stdout) File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run self.start_run(run_file,last=is_last) File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run cmd+" "+self.add_double_quote(run_file,escape_space=False)).raise_if_errors() File "~opt/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 37, in raise_if_errors raise Error(msg) RuntimeError: child process stderr output: command: 'qsub background=False nproc=20 "~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1"' /bin/sh: qsub: command not found XXXXXXXXXXXXXX Please let me know if I can share eff and log files of the run. Please advice, Kaushik -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

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FEM map calculation without model?
by Oliver Clarke 28 Apr '15

28 Apr '15

Hi all, Is there any way to apply the local map sharpening and histogram equalization procedures described as part of the FEM map generation procedure (described in “FEM: feature-enhanced map”, Afonine et al,mActa D71 2015) to an MTZ containing amplitudes and phases only, without a model (e.g. as generated by phenix.map_to_structure_factors)? I would like to see if these different approaches to map modification are useful for improving maps derived from cryoEM. I guess there is no way to do the random map perturbation part of the FEM procedure without a model, but the sharpening and histogram equalization seem like they might be applicable? Best, Oliver.

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Scientist position -- Protein Crystallization at AbbVie, North Chicago
by WEi WEi 28 Apr '15

28 Apr '15

*Scientist II, Structural Biology - Crystallization-1500000257* AbbVie (NYSE:ABBV) is a global, research-based biopharmaceutical company formed in 2013 following separation from Abbott Laboratories. The company's mission is to use its expertise, dedicated people and unique approach to innovation to develop and market advanced therapies that address some of the world's most complex and serious diseases. AbbVie employs approximately 26,000 people worldwide and markets medicines in more than 170 countries. The Structural Biology organization has an exciting opportunity for a Scientist I or Scientist II (depending on experience) to join the Crystallization group to support AbbVie's new collaboration with Calico. The Scientist will conduct biological macromolecule crystallization experiments in support of structure based drug design. The selected candidate must be knowledgeable in protein handling and characterization techniques and possess excellent communication skills. The Scientist will be expected to consistently work on multiple projects in parallel and be able to adjust to rapidly changing priorities. In addition, this individual will be highly self-motivated, able to work independently in their area of expertise and work collaboratively with cross-functional teams. For detail information, please visit the link below and apply online using the Job ID: *1500000257. * https://abbvie.taleo.net/careersection/2/jobsearch.ftl?lang=en Thanks, Wei

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Global real-space refinement
by oleg＠quantumbioinc.com 27 Apr '15

27 Apr '15

I have a question. What does trigger Global real-space refinement ? I never seen it before except one structure I am currently working on. Also I do not see any options that switch on/off "Global real-space refinement " Please advise Oleg

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Automatic linking of glycans doesn't work when hydrogens are added by ReadySet
by Tristan Croll 27 Apr '15

27 Apr '15

Hi, I'm currently using the dev 2000 version of Phenix, and noticed an issue with the automatic linking of N-linked (and presumably O-linked) glycans. If you feed a glycosylated structure sans hydrogens to Phenix and allow ReadySet to add hydrogens prior to refinement, it adds hydrogens as if the glycans are unlinked. Then, the automatic linking script rejects them due to valence issues. Cheers, Tristan

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idealizing structure
by PC 27 Apr '15

27 Apr '15

Is there a way to "idealize" a structure in Phenix? I mean, ideal omega, all residues within allowed regions of Ramachandran maps, no clashes..etc. I know it won't fit the map well but I would like to see what it looks like. Thank you. ____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium

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Re: [phenixbb] citation
by Sneha Rangarajan 27 Apr '15

27 Apr '15

Hello All, I have a non-Phenix problem- finding shape complementarity! I tried running the script for sc (ccp4) but it doesn't run to completion to give me the sc number. It stops saying "imaginary contain". What does that mean? However there is no error as such. I gave it the pdb that I got after my phenix refinement. Is there something I should be doing first to the pdb after refinement before running sc on it? Here is the script and I am also attaching the pdb. sc XYZIN F7-2_refine_113.pdb <<eof-sc MOLECULE 1 CHAIN A CHAIN B MOLECULE 2 CHAIN C eof-sc Thanks in advance!! Sneha From: Randy Read [mailto:[email protected]] Sent: Tuesday, April 21, 2015 3:42 AM To: Sneha Rangarajan Subject: Re: [phenixbb] citation Dear Sneha, Here's a link to the publication (which is open access): http://scripts.iucr.org/cgi-bin/paper?ba5210. Best wishes, Randy Read On 20 Apr 2015, at 19:02, Sneha Rangarajan <rsneha(a)umd.edu<mailto:[email protected]>> wrote: Hello, What is the correct way to cite Phenix MRage? Thanks, Sneha _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]> ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk<mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk<http://www-structmed.cimr.cam.ac.uk>

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rigid_body refinement
by Irina PROKHOROVA 24 Apr '15

24 Apr '15

Hello, how can i select two chains to be refined as one rigid body? I tried refinement.refine.sites { rigid_body = chain A and chain B } but it did not work. Irina

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on Cutting out density by Phenix
by Smith Liu 23 Apr '15

23 Apr '15

Dear All, I have tried to cut out the density by the Phenix graphical interface with the cutout type as model, but I find in the cut out map, there is more density arond the residues than in the input mtz map, here I mean, take a Lys residue as an example, in the input map, from Calpha there is about 1/2 of the sidechain was surrounded by the density, but in the cutting out map, there is about 2/3 of the sidechain was surrounded by the density. Will you please tell me if I want to get the cutting out density in the model cutout type, how can I have the cutting out density looks exactly or very close to the input density in the input mtz? Smith

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Generating cif file for DNA basepairing in PHENIX
by 李翔 22 Apr '15

22 Apr '15

Hi everyone, I am trying to build some DNA duplex models with different pitches by 3DNA. After changing the pitches from the original duplex model, I refined the duplex in PHENIX with geometry minimization. However, the basepairing get completely distorted. Is there a quick way to generate the cif file for basepairing in PHENIX or are there any other better ways to keep the basepairing restraint during the model refinement? Thank you very much for your kind help! Sincerely, Xiang -- Li Xiang Department of chemistry, University of Michigan Email：lixiang1642(a)gmail.com

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