- phenixbb - phenix-online.org

Refinement of two co-factors at the same position
by Kornelius Zeth 12 Apr '17

12 Apr '17

Dear all, I'm trying to refine the occupancy and position of two co-factors iron (III) and FEO (Fe-O-Fe) in a crystal structure. The iron (III) is placed with some occupancy on one of the iron positions in FEO. If I refine them together in Phenix with low occ phenix.refine moves the atoms apart. What is the best way of dealing with this problem? Thanks and best wishes Kornelius

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Symposium on Understanding Biology through Structure, May 13-17, 2017, Santa Fe
by Wladek Minor 12 Apr '17

12 Apr '17

Dear Colleagues, As a member of the organizing committee of "Understanding Biology through Structure", I'd like to encourage you to come to Santa Fe May 13-17 to attend this exciting Symposium. In addition to an exceptional set of talks including X-ray crystallography, cryo-EM, biochemical and biophysical methods, the Symposium will emphasize interactions between junior and senior researchers. We hope that this will present a special opportunity for junior researchers to present posters and meet senior scientists, for senior researchers to meet the next generation of structural biologists, and for all to discuss science in an informal setting. The meeting website is at https://conferences.newmexicoconsortium.org/conferences/ubts_17 and the program can be seen at https://conferences.newmexicoconsortium.org/conferences/ubts_17/program Looking forward to seeing you there, Wladek Minor -- Dr. Wladek Minor Harrison Distinguished Professor Department of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-243-2981 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1340 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908 ----

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Fwd: [ccp4bb] Join the editorial team of IUCr Journals
by Randy Read 07 Apr '17

07 Apr '17

Just in case anyone on the Phenix BB doesn't read the CCP4 one! Best wishes, Randy Read > Begin forwarded message: > > From: Louise Jones <lj(a)IUCR.ORG> > Subject: [ccp4bb] Join the editorial team of IUCr Journals > Date: 7 April 2017 at 13:23:42 BST > To: CCP4BB(a)JISCMAIL.AC.UK > Reply-To: Louise Jones <lj(a)IUCR.ORG> > > Dear All > > We are now seeking a number of new Editors and Co-editors for IUCr Journals, including our biological journals > > > > Acta Crystallographica Section D, Structural Biology > and > Acta Crystallographica Section F, Structural Biology Communications > > Full details are available at > http://www.iucr.org/news/notices/announcements/chesternotice_2017_04 > > Best wishes > Louise > _____________________________________________________ > > Louise Jones > Managing Editor > Acta Cryst. D and Acta Cryst. F > International Union of Crystallography > ________________________________________________________ ------ 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 Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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New Phenix tutorial videos
by Dorothee Liebschner 06 Apr '17

06 Apr '17

Dear Phenix users, We uploaded more videos to the Phenix Tutorial YouTube channel <https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg>: - Basic Phenix eLBOW tutorial - How to run Phaser-MR from the Phenix GUI - Explaining the atom selection syntax To give us feedback, write to tutorials(a)phenix-online.org or use the comment section in YouTube. If you are eager to see a tutorial about a certain (Phenix-related) topic, don't hesitate to tell us. Further info: To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to the channel to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button (next to the "subscribe" button). Best wishes, The Phenix team

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What happened with Rfree between dev-2376 and now?
by Mark Saper 29 Mar '17

29 Mar '17

Hi all, I’ve been running some tests with the current dev and released versions of Phenix. If I run the same job (same input files, same parameters), the current versions consistently result in Rfree values ~1% more than Phenix version dev-2376! What changed between then and now? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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Note that R-free numbers are different than a year ago.
by Mark Saper 26 Mar '17

26 Mar '17

In July 2016, I finished a refinement with Phenix dev-2376 with these final stats start final --------------------------------------- R-work: 0.1982 0.2007 R-free: 0.2376 0.2367 RMS(angles): 0.55 0.45 RMS(bonds): 0.003 0.002 Today, I reran the exact same parameter file and input files with Phenix dev-2712: start final --------------------------------------- R-work: 0.2073 0.2037 R-free: 0.2445 0.2442 RMS(angles): 0.55 0.45 RMS(bonds): 0.003 0.002 R-free values are now higher than they used to be. This fact was also flagged when I ran Table 1 today. -Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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help with pdbtools
by Edward A. Berry 25 Mar '17

25 Mar '17

1. I'm trying to use pdbtools and I don't quite get the syntax. How can I specify the output file name on the command line? these don't work: phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 output file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --output file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --file_name = shake1.pdb phenix.pdbtools --output file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5 phenix.pdbtools output.file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5 2. for the "shake" operation, is there a random seed so that it comes out differently each time? (If I do this five times with different output file names, will they all be the different?)

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DNA double helix through crystal symmetry
by wtempel 25 Mar '17

25 Mar '17

Hello, how could one restrain DNA base pairing across a crystallographic axis? Are secondary_structure.nucleic_acid restraints "symmetry-aware"? Thank you. Wolfram Tempel

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Berkeley Server Downtime (3/23 - 3/24)
by Billy Poon 24 Mar '17

24 Mar '17

Dear all, On Thursday, March 23, our servers will be shut down starting at 5:00 pm Pacific for some emergency electrical work near our building. We expect that the servers will be available the next day (3/24) by 1:00 pm Pacific. There is a possibility that the outage will last longer. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience and the short notice. -- 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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options in phenix.merging_statistics
by Murpholino Peligro 23 Mar '17

23 Mar '17

Hello. I was wondering what is the normal situation where one should click the boxes marked as "Keep anomalous pairs separate in merging statistics" (option1) and/or "Use internal variance of the data in the calculation of the merged sigmas" (option2)? I am asking because it looks like it is detrimental to the statistics, as you can see in the file attached (CSV file with 4 columns for no options, option1, option2 and option1&2). Thanks in advance. MP

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phenix ensemble ref.
by Kajander, Tommi A 23 Mar '17

23 Mar '17

Hi, is it possible to do ensemble refinement in phenix with just one domain? (and e.g. fix the other) Doens seem so? Thanks, Tommi

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Re: [phenixbb] Error running phenix.rosetta_refine tests with Rosetta 3.8
by Nigel Moriarty 21 Mar '17

21 Mar '17

Oliver My Rosetta 3.7 is 2016.32. Not sure why we are different. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Mar 21, 2017 at 8:19 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Hi Nigel, > > I tried with rosetta 3.7 (2016.46) and phenix dev-2719, and this time > compilation using rosetta.build_phenix_interface was successful (scons > finished building targets with no errors), but when I run rosetta.run_tests > it still crashes, though with a different error (see attached log). Any > ideas as to how to fix? > > Cheers > Oli > > > > On Mar 20, 2017, at 7:31 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > > Oliver > > We are currently only supporting up to Rosetta 3.7 as a c++11 compiler is > required for any subsequent versions. We have compiled using a c++11 > compiler with no problems so I suggest you revert to 3.7 or check the logs > for compilation problems. > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 <(510)%20486-5709> Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 <(510)%20486-5909> Web : CCI.LBL.gov > <http://cci.lbl.gov/> > > On Mon, Mar 20, 2017 at 9:34 AM, Oliver Clarke <olibclarke(a)gmail.com> > wrote: > >> Hi, >> >> Phenix rosetta refinement worked with previous versions of rosetta and >> phenix, but with the latest Rosetta version (3.8) and latest phenix nightly >> I get a crash when running rosetta.run_tests after building the rosetta >> phenix interface, which runs a test run of phenix.rosetta_refine. It gets >> to the stage of generating initial models and then crashes - see attached >> log. Ideas for a fix welcome! >> >> Cheers >> Oli >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > >

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Error running phenix.rosetta_refine tests with Rosetta 3.8
by Oliver Clarke 20 Mar '17

20 Mar '17

Hi, Phenix rosetta refinement worked with previous versions of rosetta and phenix, but with the latest Rosetta version (3.8) and latest phenix nightly I get a crash when running rosetta.run_tests after building the rosetta phenix interface, which runs a test run of phenix.rosetta_refine. It gets to the stage of generating initial models and then crashes - see attached log. Ideas for a fix welcome! Cheers Oli

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difference map for cryo-EM (cryo-EM map minus model map)
by Pavel Afonine 16 Mar '17

16 Mar '17

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map): Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps. One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of: (F_obs, Phase_obs) - (F_calc, Phase_calc). The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved. I'm not sure which one of the two is better. Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography). Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed. To use: phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9 which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 . If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb. In future (once fully tested) this will be integrated into phenix.real_space_refine. The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome! All the best, Pavel

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Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH; problem fixed.
by Mooers, Blaine H.M. (HSC) 15 Mar '17

15 Mar '17

Hi Andy, Thank you for the clarification! Yes, I was wrong. There is still a tools subdirectory at the top level. I installed the latest version of Rosetta from source. This is version 3.8, the Feb. 25th, 2017 release. The rosetta\_options.py file is in the same location: main/source/src/apps/public/ERRASER. Following up on your suggestion, I edited the file erraser.py in /Applications/phenix-dev-2686/modules/phenix/phenix/erraser by replacing line 543 with the following: file_path = os.path.join(params.directories.rosetta_path, 'main/source/src/apps/public/ERRASER') Phenix.erraser now runs. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…> X-ray lab (LBSF)<http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStr…> Molecular Graphics<https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/mo…> Links <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/Mo…> Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma…> office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers(a)ouhsc.edu ________________________________ From: Andy Watkins [andy.watkins2(a)gmail.com] Sent: Tuesday, March 14, 2017 11:53 AM To: Mooers, Blaine H.M. (HSC) Subject: Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH Yes, while the tools directory should still exist, the new path to ERRASER is in fact main/source/src/apps/public. I wonder if the issue lies in Phenix's subsequent interpretation of that environment variable -- i.e., the Phenix code is appending "tools/ERRASER" instead of the aforementioned path. On Mar 14, 2017 9:18 AM, "Mooers, Blaine H.M. (HSC)" <Blaine-Mooers(a)ouhsc.edu<mailto:[email protected]>> wrote: Dear phenixbb, This is a question about phenix.erraser. I had it running in March 2016, but it no longer works. I am using phenix-dev2686. I am also using the rosetta_src_2016.59086_bundle that was released in November 2016. Rosetta works fine for other tasks. I set in my bashrc file the following: export PHENIX_ROSETTA_PATH=/Users/blaine-mooers/software/rosetta_src_2016.46.59086_bundle If I use the gui or the command line, I get an error message that suggests using a relative path to the rosetta directory. This does not work either. I also tried extending the path incrementally down to the directory containing the erraser binaries. There must be some other issue. I suspect that between March and November 2016 that there has been reorganization of the directory hierarchy in rosetta. There is no longer a "tools" subfolder in the top directory. The file erraser_option.py is now located in ./rosetta_src_2016.46.59086_bundle/main/source/src/apps/public/ERRASER. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_depa…> X-ray lab (LBSF)<https://urldefense.proofpoint.com/v2/url?u=http-3A__http-3A__research.ouhsc…> Molecular Graphics<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.oumedicine.com_doc…> Links <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.oumedicine.com_doc…> Small Angle Scattering <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.oumedicine.com_docs…> office: (405) 271-8300<tel:(405)%20271-8300> lab: (405) 271-8313<tel:(405)%20271-8313> e-mail: blaine-mooers(a)ouhsc.edu<mailto:[email protected]> _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb<https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai…> Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

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phenix.erraser and PHENIX_ROSETTA_PATH
by Mooers, Blaine H.M. (HSC) 14 Mar '17

14 Mar '17

Dear phenixbb, This is a question about phenix.erraser. I had it running in March 2016, but it no longer works. I am using phenix-dev2686. I am also using the rosetta_src_2016.59086_bundle that was released in November 2016. Rosetta works fine for other tasks. I set in my bashrc file the following: export PHENIX_ROSETTA_PATH=/Users/blaine-mooers/software/rosetta_src_2016.46.59086_bundle If I use the gui or the command line, I get an error message that suggests using a relative path to the rosetta directory. This does not work either. I also tried extending the path incrementally down to the directory containing the erraser binaries. There must be some other issue. I suspect that between March and November 2016 that there has been reorganization of the directory hierarchy in rosetta. There is no longer a "tools" subfolder in the top directory. The file erraser_option.py is now located in ./rosetta_src_2016.46.59086_bundle/main/source/src/apps/public/ERRASER. Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Faculty webpage<http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…> X-ray lab (LBSF)<http://http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStr…> Molecular Graphics<https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/mo…> Links <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/Mo…> Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma…> office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers(a)ouhsc.edu

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Open Postdoctoral Position at Oak Ridge National Laboratory
by Paul Adams 10 Mar '17

10 Mar '17

Dear Colleagues, on behalf of my colleagues I’d like to bring to your attention an open postdoctoral associate position at Oak Ridge National Laboratory (ORNL): Summary - To maximize the information obtained for diffraction experiments for structural biology, data processing methods need to be improved for marginal, weak data and also for reflection overlap. Methods will be developed that make use of knowledge about the atomic model to inform data processing methods so that reflections can be successfully deconvolved. A novel technique for full profile single crystal structure refinement will be developed. This work will be performed through a National Institutes of Health (NIH) funded consortium between ORNL and Lawrence Berkeley National Laboratory (LBNL) to develop a broad range of computational tools for macromolecular neutron crystallography. The aim of this consortium is to address the need for new computational tools and methods to deal with the increasing number of neutron macromolecular structures being determined and their increasing size and complexity. These tools will be developed in close collaboration with the PHENIX program, a NIH funded consortium between several groups. Interested candidates should visit: https://www.ornl.gov/careers Job Posting: Postdoctoral Research Associate - Computational Methods for Integrating Protein Crystallography Data / NB50615195 https://recruiting-internal.ornl.gov/sap/bc/erecruiting/posting_apply?param… -- Paul Adams 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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Please attend a workshop on Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography
by Robert Sweet 08 Mar '17

08 Mar '17

Driven by recent advances in this field we will hold a workshop to discuss it. The workshop will be on Monday, May 15, 2017 at Brookhaven Nat'l Laboratory, and will be affiliated with the 2017 Users' Meeting for NSLS-II and the Center for Functional Nanomaterials. The current draft agenda is on-line here: http://usersmeeting.ps.bnl.gov/workshops/workshop.aspx?year=2017&id=136 Registration for the Workshop and Users' Meeting is here: http://usersmeeting.ps.bnl.gov/registration/?year=2017 A description of the workshop is below. The Organizers: Robert Sweet (NSLS-II, BNL), Michael Wall (LANL), Nozomi Ando (Princeton University), James S. Fraser (University of California, San Francisco), George N. Phillips, Jr. (Rice University) For answers to questions, please contact Wall: mewall(a)lanl.gov or Sweet: sweet(a)bnl.gov Description: X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins. A major focus of the workshop will be to provide a roadmap to the acquisition of reliable data by surveying measurement methods and discussing the increase in measurement accuracy enabled by improved detectors, experimental methods, and data integration. Missing from recent results is real information about the behavior of the molecules being studied that would guide the thinking of biochemists and biologists. To discuss these and their relative merits will be a second major focus of the workshop. The charge to this workshop will be to provide a roadmap to efforts that will provide the biological understanding we believe is hidden in the data. ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Deputy Director, LSBR: The Life Science and ^ (that's L Biomedical Technology Research Center at NSLS-II not 1) Photon Sciences and Biology Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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on tst_af_3.exe
by Smith Liu 07 Mar '17

07 Mar '17

Dear All, What is the function of tst_af_3.exe in Phenix? It was in category "array_family", and a antivirus software in my computer has killed it as trojan. Smith

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map_to_model space group symbol not recognized
by CPMAS Chen 06 Mar '17

06 Mar '17

Hi, All when I try to using map_to_model tool to optimize my model from low-resolution map, phenix.map_to_model refine_2.mtz seq_from_pdb.dat I got the following error, even though I did not provide ncs file, Space group symmetry written as NCS operators to ncs_from_symmetry.ncs_spec Traceback (most recent call last): File "/usr/local/phenix-1.11-2567/build/../modules/phenix/phenix/command_line/map_to_model.py", line 9, in <module> run(sys.argv[1:],out=sys.stdout) File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 5729, in run tracking_data=run_segment_and_split_map(params,out=out) File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 4931, in run_segment_and_split_map ncs_group_obj,remainder_ncs_group_obj,tracking_data=segment_map(args) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 5795, in run params,map_data,pdb_hierarchy,tracking_data=get_params(args,out=out) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2055, in get_params params=get_params_from_args(args) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2051, in get_params_from_args return command_line.work.extract() File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract value = object.extract(parent=result) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract value = object.extract(parent=result) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1122, in extract return self._type_from_words()(self.words, master=self) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/iotbx/phil.py", line 40, in from_words return sgtbx.space_group_info(symbol=str(symbol)) File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/sgtbx/__init__.py", line 97, in __init__ symbols = space_group_symbols(symbol) RuntimeError: cctbx Error: Space group symbol not recognized: <cctbx_sgtbx_ext.space_group object at 0x101836e20> Would this be a bug or I simply missed something? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Phenix.refine ignores ligand planarity restraint
by Maike Bublitz 28 Feb '17

28 Feb '17

Dear all, this has probably been discussed many times before, but I just can’t seem to find a solution for my current problem with phenix.refine: I am trying to refine a protein structure with a rather complex ligand. I’ve generated a .cif file for the ligand with eLBOW, including planarity restraints for its aromatic ring systems. However, phenix.refine keeps on distorting the 6-ring in my indole group, although all respective atoms are included in the plane definition. At a resolution of 3.0 A, I’d very much prefer to impose an ideal planar structure on this ligand. How can I convince Phenix to not distort my ligand's aromatic rings? Many thanks for your kind suggestions. Best regards, Maike ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 lab: +44 (0)1865 613318 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk>

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estimated coordinate error from phenix.refine
by Almudena Ponce Salvatierra 28 Feb '17

28 Feb '17

Dear all, I would like to know how the estimated coordinate error is calculated in phenix.refine, the one that is written on the pdb file as "ML based". I'm asking due to the following: For example if I am comparing two different models (structures determined at 2.1 and 2 Angstroms) but one does have a coordinate error estimate of 0.25 Angstroms and the other one of 0.6, respectively. Is the first model more reliable? The second one is reliable too but my question points towards how conservative or how more conservative should I be when describing distances , potential H bonds, coordination. Despite those different numbers in estimated coordinate error, the electron density maps look very similar or almost the same for both structures, very clear and complete at 2 Angstroms. That's why I was somehow surprised to find these difference. Thank you very much in advance Best Almudena -- Dr. Almudena Ponce-Salvatierra EMBL-European Molecular Biology Laboratory 71, avenue des Martyrs - CS 90181 F - 38042 Grenoble Cedex 9

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"RosettaScripts executable could not be located" error
by Yonglin Hu 24 Feb '17

24 Feb '17

Hello List, I have installed the rosetta (version 2016.32.58837) and phenix (dev-2689). I have no problem running phenix.mr_rosetta, but when I run phenix.rosetta_refine or rosetta.run_tests, I always get the following error message: Sorry: The RosettaScripts executable could not be located. Please set the environmental variable PHENIX_ROSETTA_PATH or add the appropriate directory to your PATH environment variable. But I do have relevant environmental variables set up: ROSETTA3_DB=/usr/local/rosetta_src_2016.32.58837_bundle/main/database PHENIX=/usr/local/phenix-dev-2689 PHENIX_ROSETTA_PATH=/usr/local/rosetta_src_2016.32.58837_bundle PHENIX_VERSION=dev-2689 I would appreciate it if you could tell me what really went wrong. Have a nice day, Yonglin Hu

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Phenix rosetta refine error
by pravin.jagtap＠embl.de 23 Feb '17

23 Feb '17

Hi All, I want to do phenix.rosetta refinement. I was successful in compiling rosetta and build the rosetta_refine interface. However when I try to do the refinement, I get the following error. I get the similar error in Rosetta_MR. Please let me know if you need any other information. Thanks and regards, Pravin. RuntimeError : Aborted due to error in job 1. Traceback: File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/cctbx_project/libtbx/runtime_utils.py", line 179, in run return_value = self.target() File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__ result = self.run() File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/command_line/rosetta_refine.py", line 302, in run return run(args=list(self.args)) File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 397, in run_jobs check_result(result) File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) Platform info: __FILE__ = /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos6/modules/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Feb 18 2017 __TIME__ = 00:45:46 __TIMESTAMP__ = Tue Nov 8 23:38:16 2016 __x86_64__ __linux __GNUC__ = 4 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 7 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 4.4.7 20120313 (Red Hat 4.4.7-16) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_55 PY_VERSION = 2.7.8 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 _OPENMP = 200805 gnu libc version: 2.17 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG boost/TAG: 86799 os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-3.10.0-514.6.1.el7.x86_64-x86_64-with-centos-7.3.1611-Core platform.architecture(): ('64bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 8,292,691,968 Memory free: 703,213,568 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', 'x00', 'e', 'x00', 'l', 'x00', 'l', 'x00', 'o', 'x00'] u"u00C5" = ['xc5', 'x00'] as utf-8 = ['xc3', 'x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

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eBIC and CCP-EM Spring Symposia
by Tom Burnley 21 Feb '17

21 Feb '17

Dear all, eBIC and CCP-EM are proud to announce the inaugural symposium of eBIC, the UK national cryoEM centre at Diamond Light Source, and the third CCP-EM Spring Symposium on April 24–26, 2017. This three day conference will be held at the Diamond/RAL Campus, Harwell, Oxfordshire. The eBIC opening symposium will be on the first day, highlighting the advances of cryoEM and feature presentations with an emphasis on emerging and challenging technologies, followed by CCP-EM featuring of state-of-the-art presentations related to cryo-EM methods and applications. Confirmed speakers include: eBIC Speakers: Yifan Cheng, UCSF School of Medicine John Briggs, MRC Laboratory of Molecular Biology Lori Passmore, MRC Laboratory of Molecular Biology Radostin Danev Max Planck Institute of Biochemistry Greg McMullan, MRC Laboratory of Molecular Biology Sharon Wolf, Weizmann Institute of Science CCP-EM Speakers: Piet Gros, Utrecht University Maya Topf, Birkbeck / UCL David Waterman, STFC Tanmay Bharat, MRC Laboratory of Molecular Biology / University of Oxford Paul Adams, Lawrence Berkeley National Laboratory Tristan Croll, University of Cambridge Erik Lindahl, SciLifeLab Kay Grunewald, STRUBI Carolyn Moores, Birkbeck / UCL Morgan Beeby, Imperial College London Rob Nicholls, MRC Laboratory of Molecular Biology Ausra Domanska, University of Helsinki Becky Thompson, University of Leeds Full details and registration for the conference is provided here: http://www.ccpem.ac.uk/training/spring_symposium_2017/spring_symposium.php http://www.diamond.ac.uk/Home/Events/2017/eBIC-CCP-EM-Symposium.html Places are limited and registration will be on a first come first serve basis. We look forward to seeing you in April, Peijun, Tom & Colin and the rest of the eBIC and CCP-EM teams http://www.diamond.ac.uk/Science/Integrated-facilities/eBIC.html http://www.ccpem.ac.uk/ -- Dr Tom Burnley, PhD CCP-EM | @ccp_em | www.ccpem.ac.uk Science and Technology Facilities Council (STFC) The Research Complex At Harwell Rutherford Appleton Laboratory, R92 OX11 0FA 01235 56 7871

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