- phenixbb - phenix-online.org

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

2 5

Re: [phenixbb] phenix.erraser and PHENIX_ROSETTA_PATH; problem fixed.
by Mooers, Blaine H.M. (HSC) 16 Mar '17

16 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]>

2 1

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

1 0

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 ] --

2 1

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) =========================================================================

1 0

on tst_af_3.exe
by Smith Liu 08 Mar '17

08 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

1 0

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 ******************************************************

2 2

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>

8 13

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

3 2

"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

2 1