- phenixbb - phenix-online.org

SAD Phasing
by Rajagopalan, Senapathy 13 Apr '10

13 Apr '10

Hi Everyone, I have been trying to solve a structure of a protein-DNA complex using SAD data, but am running into problems and have some questions on how phenix solves it. From Mathews coefficient calculation, I know that my protein binds to the DNA as a dimer in the asymmetric unit. And when I use this information to specify the the number of heavy atoms to look for, I always get more (1.5-2X, depending on what resolution cutoff I use) in the final heavy atom sites pdb file. More importantly, the map looks 'incomplete' in the sense that part of one of the strands in the double stranded DNA is missing. My question is if this is the result of phenix using some incorrect sites (such as with low occupancy) while phasing. If so, then how can I fix it. I have tried deleting the low occupancy sites and reading the edited heavy atom sites file explicitly using sites_file=ha.pdb, but it doesn't seem to help. Also, if I just use solve to find the heavy atom sites, those tend to be different too... Any suggestions here would be appreciated. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Group ADP syntax question
by Peter Grey 13 Apr '10

13 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 08 Apr '10

08 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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