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Problem with Molprobity analysis in phenix 1.6.4
by Mark A Saper 23 Dec '10

23 Dec '10

I am running phenix 1.6.4-486 with GUI and obtained high clash scores in the Molprobity calculations done by phenix.refine. I think I know why after doing some experiments with the current Molprobity running at http://molprobity.biochem.duke.edu/. If I take my well-refined structure as output by phenix (.pdb) and use it directly on the Molprobity web site, the clash score is much lower: 2.75 for 39 total bumps. Many of these involve residues or waters with high B factors. If I first remove all hydrogens from the phenix-refined .pdb file with a text editor, and upload it to the Molprobity web site, then add hydrogens, and then calculate clash score, the score is now 8.69 or 123 bumps for 14150 atoms. This is *identical* to what phenix calculates. Therefore, why doesn't phenix feed the refined coordinates directly into the Molprobity (probe) calculations? Has this change been made in one of the nightly builds? Thanks, Mark Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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Fwd: Fourth annual CCP4 summer school in USA, at APS, June 7-15
by Nathaniel Echols 22 Dec '10

22 Dec '10

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: <phenixbb(a)phenix-online.org> Date: Wed, 22 Dec 2010 11:02:15 -0600 Subject: Fourth annual CCP4 summer school in USA, at APS, June 7-15 Dear Colleagues, Building on the success of the past 3 years, we are pleased to announce the fourth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2011/index.php Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 7 to 15. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 8. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2011/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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ADP restraints - distance power, average power, etc
by Joseph Noel 21 Dec '10

21 Dec '10

Hi All, I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)? I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2. Thanks! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Re: [phenixbb] ADP restraints - distance power, average power, etc
by Joseph Noel 20 Dec '10

20 Dec '10

Dear Ed, Thanks so much for the suggestion about REFMAC but I seemed to have found out the issue. The positive density on Met sulfurs and backbone carbonyls and amide NHs does not appear when I calculate a "normal" sigmaa weighted mFo-dFc map. The positive density was appearing only when I checked the kicked map option. So the "extra" density seems to be due to generating kicked maps. Sorry about the confusion related to the sigma level. Just meant that the positive density was not insignificant in the kicked mFo-dFc maps. Density was visible on these specific areas starting around 3.5-4.0 sigma and visible in several places contoured up to 8 sigma. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________ On Dec 20, 2010, at 12:00 PM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. ADP restraints - distance power, average power, etc (Joseph Noel) > 2. Re: ADP restraints - distance power, average power, etc > (Ralf W. Grosse-Kunstleve) > 3. Re: ADP restraints - distance power, average power, etc > (Pavel Afonine) > 4. Secondary structure restraints - where to specify file using > GUI? (Luke Rice) > 5. Re: Secondary structure restraints - where to specify file > using GUI? (Nathaniel Echols) > 6. Re: ADP restraints - distance power, average power, etc > (Joseph Noel) > 7. Re: ADP restraints - distance power, average power, etc > (Joseph Noel) > 8. Re: ADP restraints - distance power, average power, etc > (Ed Pozharski) > 9. Re: Secondary structure restraints - where to specify file > using GUI? (Luke Rice) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 19 Dec 2010 12:58:43 -0800 > From: Joseph Noel <noel(a)salk.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] ADP restraints - distance power, average power, > etc > Message-ID: <2E132727-1B34-4ED5-98DA-2210B7D1FF48(a)salk.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > > I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)? > > I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2. > > Thanks! > > Joe > ___________________________________________________________ > Joseph P. Noel, Ph.D. > Investigator, Howard Hughes Medical Institute > Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics > The Salk Institute for Biological Studies > 10010 North Torrey Pines Road > La Jolla, CA 92037 USA > > Phone: (858) 453-4100 extension 1442 > Cell: (858) 349-4700 > Fax: (858) 597-0855 > E-mail: noel(a)salk.edu > > Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 > Web Site (HHMI): http://hhmi.org/research/investigators/noel.html > ___________________________________________________________ > >

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phenix.refine with simulated annealing
by zhangh1＠umbc.edu 17 Dec '10

17 Dec '10

Hi there, I was trying to perform a SA refinement for PDB# 2VZ8 using the following phenix script: random_seed=2679941 phenix.refine 2VZ8.pdb 2vz8.mtz simulated_annealing=true main.random_seed=${random_seed} output.prefix=${random_seed} >${PDB}-phx-sa.log where 2VZ8.pdb was downloaded from rcsb, and 2vz8.mtz was converted from the cif file by ccp4-cif2mtz. But it ended up with: ******************* =============================== refinement start ============================== Traceback (most recent call last): File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 229, in refinement_machine xray_structure = model.xray_structure,) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 133, in extract_from_pdb_header xray_structure = xray_structure) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/cctbx_project/mmtbx/f_model.py", line 302, in __init__ twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144) RuntimeError: cctbx Error: Parse error: unexpected character: NULL ************************ I tried another smaller system and it works well. Not sure what happens, and thanks for any suggestion! Hailiang

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phenix.map_to_object for HA sites
by Michael Hothorn 16 Dec '10

16 Dec '10

Hi, I have a .pdb with heavy atoms that are dispersed all over the unit cell. I would like to move all of them (about 40) as close as possible to my refined structure. Could phenix.map_to_object do that for all heavy atoms at once, or would I need to do this in an atom by atom manner? Thanks Michael

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Map filenames are not honored [dev-610]
by Schubert, Carsten [PRDUS] 16 Dec '10

16 Dec '10

Hi, I just noticed that v610 does not honor map file names defined in the .def file. Instead it constructs its own file name from the prefix, serial and map_type settings. That works fine for run-of-the-mill fofc and 2fofc maps, but causes a clash in map filenames when one also computes kicked maps or other maps with non-default settings beside the default fofc and 2fofc maps. Cheers, Carsten

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phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups
by Joseph Noel 15 Dec '10

15 Dec '10

Pavel or Nat, Can you point me to the button in the GUI to use to run this? I am pretty much a GUI guy although not adverse to running things through the command like like the old days (yes, I was a command like geek when I started at Yale in 1990 and until I stopped (temporarily) doing anything worthwhile around 2001. Now that I am back in the lab doing work (but probably still not worthwhile) I have become addicted to GUIs and buttons. Blame my daughters! LOL Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups
by Pavel Afonine 15 Dec '10

15 Dec '10

PHENIX users: starting dev-610 (development version of PHENIX) there is a new tool available for completely automated partitioning a model into TLS groups: http://www.phenix-online.org/download/nightly_builds.cgi To run: phenix.find_tls_groups model.pdb or if you have a multiple CPU machine: phenix.find_tls_groups model.pdb nproc=N where N is the number of CPUs available (thanks Nat for parallelization!). There is no parameters that a user is supposed to tweak (except defining the number of CPUs, if desired). The result of running the above command are atom selections that define TLS groups. These atom selections are ready to use in phenix.refine. This is available from PHENIX GUI too, where automatically defined TLS groups can be readily visualized and checked on the graphics (thanks Nat!). The algorithm is fast. For example, for a GroEL structure (3668 residues, 26957 atoms, 7 chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 CPUs. Analogous job takes 3630 seconds using TLSMD server. For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 seconds using 10 CPUs. The timing results may vary depending on the performance of your computer. There is ongoing work that will slightly improve phenix.find_tls_groups within the next few weeks / a month; however the current version is functional and can be tried now. An example of such improvements are analyzing (scoring) user-defined TLS groups (for example, TLS groups from PDB file header), automated combining cross-chain TLS groups (non-contiguous segments) that will be obtained through connectivity analysis, better handling non-protein chains, and more. Integration with phenix.refine is also planned. Any feedback is very much appreciated! Thanks, Pavel.

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request for openmp compile comments
by Bryan Lepore 14 Dec '10

14 Dec '10

if anyone has specifically gotten automr to run on an openmp-compiled phenix installation with something like the specs i give below, i would appreciate any details you could offer. (in my hands, automr always crashes, refine works.) -Bryan any recent nightly release with --openmp gcc/g++ 4.4.5 (or thereabouts) 2.6.35-23-generic SMP i686 (or thereabouts) amd, intel, (or thereabouts) Ubuntu (recent - but not Fedora)

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