April 2010 - phenixbb - phenix-online.org

Group ADP syntax question
by Peter Grey 12 Apr '10

12 Apr '10

Hi Phenix people, Is it possible to have One B-factor per residue for one part of the structure and for other parts to use One isotropic B per selected group of atoms. For example to have one B-factor for the entire chain A and have One B-factor per each residue in chain B ? Thanks, -- Peter

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sculpt program
by sbiswas2＠ncsu.edu 12 Apr '10

12 Apr '10

Dear all, I was trying to generate a model using the sculpt program in phenix. when I run it with both alignment file and pdb file I get the following message: Processing PDB... Next model: ''... Next chain 'A'... No matching alignment for chain 'A'; delete PDB output requested Executing design... Everything is deleted; output file empty Any help with this... thanks, Shya

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assert n_ncs > 0
by Robert Ng 12 Apr '10

12 Apr '10

Hi again, How about this one ... Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 71, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 413, in __init__ self.process_ncs_restraint_groups() File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 672, in process_ncs_restraint_groups log = log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 306, in from_atom_selections log=log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 219, in __init__ assert n_ncs > 0 AssertionError Thanks again, Robert

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Optimization of the mask parameters in PHENIX
by Pascal Egea 12 Apr '10

12 Apr '10

Dear All, I am using the latest Phenix version (356) with the GUI and I would like to see the effect of optimization of the mask parameters. How can I do this with the GUI in the latest version ( I am also using the secondary structure restraints) in the manual I can see the command line phenix.refine model.pdb data.mtz optimize_mask=true however I don't see such option in the GUI (I can't see it listed in the whole list of commands) Thanks in advance -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pegea(a)mednet.ucla.edu

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Superimposing homologues
by Young-Jin Cho 09 Apr '10

09 Apr '10

Hi Phenix users, I am wondering if phenix or other program provide superimposing pdb files as best as possible(!) I used Superpose in CCP4 but only worked for same sequence of pdb files. So my first question is how I can superimpose more than two different pdb files that are homologues (including water or not). Of course you can do similar thing in coot or pymol, but I wonder if we have better ways to do this kind of job. Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing. Thirdly, if I have 10 different structures, is there any way to superimpose into such as a calculated average structure of them and fit others into this averaged structure for better comparison? As always, thanks in advance, Young-Jin

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fix rotamers
by Robert Ng 09 Apr '10

09 Apr '10

Dear all, I want to do fix rotamers with the phenix with my 3A resolution virus data. Just do some try out. But I got the memory error listed below: Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 1170, in run call_back_handler = call_back_handler) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/strategies.py", line 570, in refinement_machine params = params.fit_side_chains) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/refinement/fit_rotamers.py", line 779, in run map_sel = flex.abs(residual_map_data) < params.filter_residual_map_value MemoryError Does anybody has this problem before ? and know how to fix this ? Robert

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applying B_factor and scale correction to an MTZ
by Francois Berenger 09 Apr '10

09 Apr '10

Hello, Is there a tool to apply both the scale and overall B-factor correction found by the wilson plot to a given MTZ file? After applying these corrections, is there another way than redoing wilson to check that the output MTZ is on absolute scale? Thanks a lot, Francois.

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Re: [phenixbb] Superimposing homologues
by Thomas C. Terwilliger 08 Apr '10

08 Apr '10

Hi Young-Jin, phenix.superpose_pdbs fixed.pdb moving.pdb will do all these things for you except making the average structure. All the best, Tom T >> Hi Phenix users, >> I am wondering if phenix or other program provide superimposing pdb files >> as best as possible(!) >> I used Superpose in CCP4 but only worked for same sequence of pdb files. >> >> So my first question is how I can superimpose more than two different pdb >> files that are homologues (including water or not). Of course you can do >> similar thing in coot or pymol, but I wonder if we have better ways to do >> this kind of job. >> Secondly, if things working, to do better superimposition, is it possible >> to input core domain residues information vs. flexible residues >> information while superimposing. >> Thirdly, if I have 10 different structures, is there any way to >> superimpose into such as a calculated average structure of them and fit >> others into this averaged structure for better comparison? >> >> As always, thanks in advance, >> >> Young-Jin >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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OpenMP incompatible with Phenix GUI?
by Donnie Berkholz 07 Apr '10

07 Apr '10

Dear developers, I would really like to use OpenMP parallelization and also use the Phenix GUI. When I attempted a source build with OpenMP support, I was informed that the two were incompatible. My understanding is that this used to work fine with the old wizards. Would it be possible to fix this? -- Thanks, Donnie Donald S. Berkholz, Postdoctoral research fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Medical Sciences 2-66 Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 612-991-1321

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Re: [phenixbb] phenixbb posting
by Leonid Flaks 07 Apr '10

07 Apr '10

Nathaniel Echols wrote: > The server bounced your message - are you subscribed to the list? > FYI, I'm not sure why firefox won't start here; sometimes it gets > confused by Phenix's copy of GTK, but that's not what the error > message looks like. You can try opening the Preferences in Phenix, > select the "File handling" parameters, and check "Reset > LD_LIBRARY_PATH for external apps". Let me know if that doesn't fix > the problem. > > thanks, > Nat > > ---------- Forwarded message ---------- > From: Leonid Flaks <flaks(a)bnl.gov <mailto:[email protected]>> > To: phenixbb(a)phenix-online.org <mailto:[email protected]> > Date: Wed, 07 Apr 2010 15:51:11 -0400 > Subject: problem with firefox and phenix-1.6.1-357 > I installed phenix-1.6.1-357 on Fedora-12. If I click on the question > mark in the GUI, I see the following: > > Using browser /usr/bin/firefox > /usr/lib/firefox-3.5.9/firefox: symbol lookup error: > /usr/lib/libgnome-2.so.0: undefined symbol: g_dgettext > > > and firefox would not start. I saw similar errors reported more then a > year ago, but that is a new fedora-12 installation. > > Any ideas? > > > Thanks, > > Leon > > Yes, I realized that I need to subscribe first, which I did after sending my message ;-) I tried to follow your advice - checked the box, but nothing changed. Same error message. -- Leon

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