- phenixbb - phenix-online.org

DNA covalent bond angles deviate from PDB standard dictionary
by Scott Classen 05 Jan '11

05 Jan '11

Hello, I'm running into validation problems with DNA when validating on PDB website. the validation report indicates that the refined value is significantly different that the PDBs standard dictionary. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard Name ID Number Angle Value Deviation ------------------------------------------------------------------------------------------- 2.2 DG D 6 N9 - C1' - O4' 110.5 108.3 0.3 2.6 DC D 7 N1 - C1' - O4' 110.9 108.3 0.3 2.3 DC D 8 N1 - C1' - O4' 110.6 108.3 0.3 3.0 DT D 9 N1 - C1' - O4' 111.3 108.3 0.3 I've looked through a few of these in the .geo file and it appears that phenix.refine is using different values. for example, angle pdb=" O4' DG D 6 " pdb=" C1' DG D 6 " pdb=" N9 DG D 6 " ideal model delta sigma weight residual 108.40 110.18 -1.78 3.00e+00 1.11e-01 3.52e-01 ideal is specified as 108.4º so clearly my refinement has converged, but it has NOT converged on the RCSBs accepted value of 110.5º What to do? Who is "right" phenix or RCSB? Thanks, Scott

3 2

bugs in dev 625
by Weiergräber, Oliver H. 05 Jan '11

05 Jan '11

Hello, trying to use phenix.autobuild (command line version, didn't try the gui) in dev 625, I encountered the following error: ############################################ Build cycle 1 of 6 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 No refinement carried out (may need free R flags) Error message from phenix.refine: global name 'libtbx' is not defined Refinement failed... ############################################ If invoked directly, phenix.refine seems to run fine, so there may be a problem with scripting in the autobuild wizard. Regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institut für Strukturbiologie und Biophysik ISB-3: Strukturbiochemie Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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viewing maps in xfit
by David Shin 05 Jan '11

05 Jan '11

Hi - Anyone have a script to convert phenix .mtz output so I can read in maps in xfit? I still find xfit handy for a few things. D

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errors when disabling Rfree
by chene＠umbi.umd.edu 03 Jan '11

03 Jan '11

Dear Phenixers, I have a low resolution twinned data, for which I disabled cross validation in refinement. The refinement worked and exported the refined coordinates. However, the phs files for maps are empty and there were such errors as below. It seems the free set is required for maps. I wonder how to fix this problem? Thanks Chen Traceback (most recent call last): File "/home/chene/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 "/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 103, in run map_manger.write_files() File "/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1281, in write_files fmodel = self.refine_object.fmodels.fmodel_xray(), params = mtz_mc) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/maps/__init__.py", line 290, in map_coefficients_from_fmodel centrics_pre_scale = params.centrics_pre_scale) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1780, in map_coefficients w2 = w2) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1695, in map_coefficients sigmaa_object = self.sigmaa_object( detwinned_data=dt_f_obs,f_model_data=tmp_f_model, tmp_free=tmp_free,forced_update=True) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1504, in sigmaa_object kernel_width_free_reflections=200, File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/scaling/sigmaa_estimation.py", line 131, in __init__ raise RuntimeError("No free reflections.") RuntimeError: No free reflections. Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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Automated Mg & K ions picking
by Hasan Demirci 02 Jan '11

02 Jan '11

Hi, I have a low resolution data and I am trying to place Mg++ and K+ ions. As far as I know for ligand search at least 3 atoms required. Is it possible to do an automated search of these single atom ions by using phenix similar to automated water picking protocol? Thanks. -- Hasan DeMirci, Ph.D. Postdoctoral Fellow Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 185 Meeting Street Providence, RI 02912 (401) 863-3652 lab (SFH) (401) 863-6124 lab (ship st) (401) 226-7852 cell Hasan_DeMirci(a)Brown.edu demircha99(a)gmail.com

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MACOSX_DEPLOYMENT_TARGET mismatch between PHENIX and Coot
by Ben Eisenbraun 30 Dec '10

30 Dec '10

Howdy PHENIXians, One of my users reported this error: File "/programs/i386-mac/coot/coot-latest/lib/python2.7/sysconfig.py", line 300, in _init_posix raise IOError(msg) IOError: $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.4" but "10.5" during configure The person is running on OS X Intel, using a PHENIX nightly and trying to call Coot. It looks like the PHENIX nightlies are built with MACOSX_DEPLOYMENT_TARGET=10.4, and the Coot I built used M_D_T=10.5 and Python is unhappy about this. It's easy to test this: $ export MACOSX_DEPLOYMENT_TARGET=10.3 $ phenix.python Traceback (most recent call last): File "/programs/i386-mac/phenix/dev-606/phenix-dev-606/build/mac-intel-osx/base/Python.framework/Versions/Current/lib/python2.7/site.py", line 553, in <module> <snip> IOError: $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.3" but "10.4" during configure Or if you have access to one of our installations: $ phenix.python import os os.system('coot') Results in the original error pasted above. After playing a bit, I came up with a workaround. If you just set the M_D_T to 10.5 before starting Coot and _after_ starting PHENIX, it all seems to work. E.g. I can start Coot using this script: $ cat coot.py #!/usr/bin/env phenix.python import os os.putenv('MACOSX_DEPLOYMENT_TARGET', '10.5') os.system('coot') And since the 'coot' binary in the PATH is a wrapper script, I can just set it in the environment there. My question is: does Python actually need this? Is my workaround going to break something? I'm not enough of a Pythonista to be able to tell from looking at the sysconfig code if this will be an issue. There is a comment in the source: # On MacOSX we need to check the setting of the environment variable # MACOSX_DEPLOYMENT_TARGET: configure bases some choices on it so # it needs to be compatible. But it's not clear to me when it's going to be used. I'm almost certainly going to implement the workaround, so I'm mostly posting this for the list archives and to see if anyone has a better idea. Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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LigandFit (distorted manesium hexahydrate cluster)
by Hasan Demirci 28 Dec '10

28 Dec '10

Dear All, I am trying to run " LigandFit " with the following hydrated magnesium hexahydrate cluster (without the hydrogens) pdb. "HETATM 7 MG MG6 A 1 -53.936 117.342 91.273 1.00128.70 A MG HETATM 2 O1 MG6 A 1 -55.351 117.224 89.749 1.00128.62 A O HETATM 3 O2 MG6 A 1 -52.532 117.421 92.718 1.00127.25 A O HETATM 4 O3 MG6 A 1 -55.370 118.284 92.428 1.00127.74 A O HETATM 5 O4 MG6 A 1 -53.253 119.219 90.518 1.00128.43 A O HETATM 6 O5 MG6 A 1 -54.385 115.379 91.937 1.00127.84 A O HETATM 7 O6 MG6 A 1 -52.566 116.391 89.994 1.00128.62 A O " LigandFit automatically runs the elbow and creates a new search pdb file with hydroges and while doing this, elbow totally screws up the original starting geometry of the Oxygen atoms within the cluster after the addition of hydrogens. "HETATM 1 MG MG6 A 1 -53.913 117.323 91.231 1.00128.70 A MG HETATM 2 O1 MG6 A 1 -55.140 117.947 90.141 1.00128.62 A O HETATM 3 O2 MG6 A 1 -53.080 118.061 92.589 1.00127.25 A O HETATM 4 O3 MG6 A 1 -55.453 117.480 92.061 1.00127.74 A O HETATM 5 O4 MG6 A 1 -52.768 118.528 90.669 1.00128.43 A O HETATM 6 O5 MG6 A 1 -53.676 115.727 91.923 1.00127.84 A O HETATM 7 O6 MG6 A 1 -53.363 116.194 90.004 1.00128.62 A O HETATM 8 H11 MG6 A 1 -55.461 117.161 89.473 1.00128.62 A H HETATM 9 H21 MG6 A 1 -52.333 117.378 92.967 1.00127.25 A H HETATM 10 H31 MG6 A 1 -55.430 118.350 92.700 1.00127.74 A H HETATM 11 H41 MG6 A 1 -53.300 119.422 90.378 1.00128.43 A H HETATM 12 H51 MG6 A 1 -54.636 115.255 92.077 1.00127.84 A H HETATM 13 H61 MG6 A 1 -52.319 116.372 89.793 1.00128.62 A H " Is it a bug or am I making something wrong? Does the search pdb HAVE TO be covalently linked? or can I search for a cluster? Thanks. -- Hasan DeMirci

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ramachandran_restraints
by José Trincão 28 Dec '10

28 Dec '10

Dear all, I am refining a structure to 2.9 A, with pretty bad experimental data (P1, ~5400 residues in the A.U. (4 mol), anisotropic, fairly incomplete...). I have been running phenix.refine with NCS, 1 ADP per residue, lower target weights, TLS. My R/Rfree are stuck at about 2.4/3.05. I was getting around 2% ramachandran outliers at every cycle so I have been giving the nightly builds a shot. Now I get 0.2% outliers without changing any parameters for the ramachandra_restraints but it is forcing some of the peptide bonds out of the density. What can I tweak to improve the refinement? Thanks all in advance! Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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Re: [phenixbb] Simple Phaser Question (Ed Pozharski
by Joseph Noel 27 Dec '10

27 Dec '10

Hi Ed, Yes, that is what I generally do but it sometimes is a slightly different so I wanted a more general approach. 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 25, 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. Simple Phaser Question (Joseph Noel) > 2. Re: Simple Phaser Question (Ed Pozharski) > 3. Questions about phenix.refine with twin_law (Keitaro Yamashita) > 4. Re: Questions about phenix.refine with twin_law (Peter Zwart) > 5. Re: Questions about phenix.refine with twin_law (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Dec 2010 17:11:37 -0800 > From: Joseph Noel <noel(a)salk.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Simple Phaser Question > Message-ID: <5E3B81ED-4C13-488E-8C28-33DB29263AEF(a)salk.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > > I am working with a protein that is a physiological dimer. On occasion I obtain a unit cell with one monomer in the asymmetric unit but most often I obtain an enantiomorphic space group with an expanded C axis that contains two molecules in the asymmetric unit. Anyway, that is all moot to some extent. I am wondering if for the case of my NCS dimer, is there a way using Phaser in Phenix to ensure that when both monomers are found, they are "close together" representative of the physiological dimer? When I search with individual monomers I often obtain a solution with two monomers but in different asymmetric units. Of course, I could easily do the transformation to form the physiological NCS dimer for later refinement but just wondering if I could avoid this from the get go with the appropriate Phaser keyword input (GUI if possible). > > Thanks and Happy Holidays! > > 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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Simple Phaser Question
by Joseph Noel 25 Dec '10

25 Dec '10

Hi All, I am working with a protein that is a physiological dimer. On occasion I obtain a unit cell with one monomer in the asymmetric unit but most often I obtain an enantiomorphic space group with an expanded C axis that contains two molecules in the asymmetric unit. Anyway, that is all moot to some extent. I am wondering if for the case of my NCS dimer, is there a way using Phaser in Phenix to ensure that when both monomers are found, they are "close together" representative of the physiological dimer? When I search with individual monomers I often obtain a solution with two monomers but in different asymmetric units. Of course, I could easily do the transformation to form the physiological NCS dimer for later refinement but just wondering if I could avoid this from the get go with the appropriate Phaser keyword input (GUI if possible). Thanks and Happy Holidays! 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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Non-standard residue numbers in NCS restraints
by Sampson, Jared 23 Dec '10

23 Dec '10

Greetings all, My lab is working on a 3.2Å resolution structure with 6 NCS copies of an antibody Fab fragment with insertions in its CDR loops. The residue numbers of CDR loop H3, for example, include 100A, 100B, etc. in each of the heavy chains (Kabat numbering). There are observable differences between NCS copies in parts of the model due to crystal contacts and so forth, so we want to exclude those residues from the NCS. Phenix.refine, when given NCS restraints like the example below, produces a result with much higher R/Rfree values than when the same structure was run with "normal" continuous numbering (R/Rfree of .26/.30 compared to .21/.26 before changing to Kabat numbering). Reference selection: chain H and (resseq 1:100A or resseq 100H:113) Restrained selection: chain I and (resseq 1:100A or resseq 100H:113) Phenix version is 1.6.4-486. Any thoughts on what might be causing this or how to account for the non-standard numbers in NCS restraints? Thanks, Jared Sampson -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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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 18 Dec '10

18 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 17 Dec '10

17 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 16 Dec '10

16 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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phenix.refine use_experimental_phases vs target=mlhl
by Francis E Reyes 14 Dec '10

14 Dec '10

Are these settings redundant? i.e. what happens when you have target=mlhl, use_experimental_phases=False? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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AutoSol/PhaserSAD with more than one anomalously-scattering atom produces error...
by Francis E Reyes 13 Dec '10

13 Dec '10

Hi all I'm getting an error... "'InputEP_SAD' object has no attribute 'addSCAT_TYPE'" from autosol. Facts: - phenix-1.6-289 - SAD experiment with two types of anomalous scatterers in the xtal, data is the peak wavelength of one of the anomalous scatterers. - sites are input from a previous phaser run (ha_x.pdb_formatted.pdb) - the atom positions are likely correct, but the atom types are all the same atom (I'd like phenix/phaser to go through the list and reannotate/refine based on the proper heavy atom identities) - additional atom types/f'/f'' defined in autosol.eff, Using the documentation example "SAD with more than one anomalously-scattering atom" (http://www.phenix-online.org/documentation/autosol.htm). Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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changing test set flag
by Michael Hothorn 11 Dec '10

11 Dec '10

Dear all, I used phenix.refine to generate the test set flag for my dataset which it did with a value of 1. I now use a program that expects the test set flag in the mtz file to be 0. Is there a simple way to change the flag from 1 to 0 keeping the flagged reflections identical? Thanks! Michael

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Help needs: SAD-phasing for Cobalt ion
by YoungJin 10 Dec '10

10 Dec '10

Dear helpers in phenix, I have anomalous data (Co; wavelength: 1.609A) that I want to use its Phase information from SAD-phasing method (autosol). As I have a native data (from nomal wavelength ~1A) with higher resolution (~2A) than SAD data (~2.5A), I wanted to apply phase information to this native data for further refinement: My goals were 1. I want to confirm where is my heavy metal is; 2. I want to refine further using native data as has higher resolution. At first, when I did autosol, it didn't give me perfect result. So far what I tired is as following: 'SAD peak' from imosflm generated mtz file (scaled), 'Phases' from first refmac generated mtz file from the native data, and 'MIR native' from the native data mtz file (imosflm and scaled). FOM: 0.186; overall score was 10.75 +/- 12.33. FYI. I input 2 sites and result suggested 3 sites. Each molecule has one binding site of metal ion. I was using old Mac version:1.6.4-486 Anyway, I simply passed the result over Autobuild. It ran and gave me better statistics as following: R/Rfree=0.2734/0.3312; CC 0.76. However (I have two molecules/ASU) one of models was not great. But this time, anomalous density map well phased(?!) to 2Fo-Fc map and I could see - it was before only one heavy metal I clearly could see- 2 heavy metal signal from 2 molecules and those positions are well matched with native density maps. So I continued phenix.refine using Autobuild made 'expt_fobs_phase_freeR_flags_1.mtz'. The question is the statistics from anomalous data itself (it has slight dispcrepancy between anomalous map and 2Fo-Fc/Fo-Fc map due to phase problem) or even those from native data is better than my current model which came from native data set (SAD-phased as described above) with higher resolution. I think one of main reasons is one of molecule has a lid that does not perfectly fit into current density map. However, in terms of heavy metal position and the active site is better from current map (Autobuild generated model). FYI: current model has R/Rfree=0.21/0.27(best was 0.21/0.26); 0.19/0.24 (for native data only used model) .... Am I too concerning for statistics or is there something I am missing? Now my questions are as following plus any suggestions are welcome: 1. For SAD-phasing, could you tell me which is best way to do so with my case (one data from the edge of heavy metal (lower resolution) and native data (higher resolution) or where is the point I can convince. Also I tried to use DANO/SIGDANO column (from hkl2000 and ccp4) but seems like it (Autosol) doesn't take them into account. Could you tell me how can I improve phase by using anomalous data? 2. In case of Co, does anyone have experience about coordination numbers? I thought it should have 6 (or 4) coordination numbers. The question what I have now is about the numbers and their lengths ... I though it should be within 2A, but not true for my current models (And somehow distorted octahedron or else with 2.07-3.28A). I also searched PDB files, and found that many deviations from 1.98 to 2.82A (depending on corresponding atoms and resolutions: 3KOI, 3KON, 2DD5, and 2XJM). I would appreciate if you can give me any tips regarding this issue. Many thanks in advance, Young-Jin

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