March 2007 - phenixbb - phenix-online.org

Re: [phenixbb] Few questions -- FreeR flag specification
by Tom Terwilliger 16 Mar '07

16 Mar '07

Hi John, I'm sorry for the slow reply; I was on a site visit and out of email contact. The AutoBuild wizard in the current version (which I am afraid you probably do not have!) does try to take the FreeR flags from your input file. You can also tell it specifically to do so with the GUI and in the command-line with refinement_file=ref.mtz input_refinement_labels="FP SIGFP None None None None None None FreeR" If you have version 1.25a , then you still should be able to specify the column for FreeR flags in the GUI window that asks which column labels to use (I could be wrong about that, however, as I don't have this version on my computer any longer). You should also be able to specify them with a script: phenix.runWizard AutoBuild AutoBuild.start_from_model terwill@rosie> cat $PHENIX/phenix/phenix/wizard_scripts/AutoBuild.start_from_model # AutoBuild.start_from_model # script to run a AutoBuild starting from a model # Version 1.26 of 26-Jan-2007 # run with: # phenix.runWizard AutoBuild AutoBuild.start_from_model [restart] # if you specify restart it will forget everything, # otherwise it will continue on from where it is now. input_ncs_file NONE # heavy-atom or PDB file for finding NCS input_data_file $PHENIX/examples/p9-sad/solve_1.mtz # file with experimental data. # Can be any format if only FP SIGFP; must be mtz if phases or HL or FreeR input input_labels FP SIGFP None None None None None None FreeR_flag # optional # line defining the 9 columns in input_mtz_file corresponding to # FP SIGFP PHIB FOM HLA HLB HLC HLD FreeR (use "None" for missing) input_map_file $PHENIX/examples/p9-sad/resolve_1.mtz # Optional map-coefficients file for first rebuild input_map_labels FP PHIM FOMM # optional line defining the 3 columns # in input_map_file corresponding to FP PHIB FOM ("None" for missing) input_seq_file $PHENIX/examples/p9-sad/seq.dat # file with sequence in 1-letter form # separate chains with >>> resolution 2.5 # high-resolution limit solvent_fraction 0.60 # you can put any other parameters here input_pdb_file $PHENIX/examples/p9-sad/p9.pdb # input PDB file for rebuilding rebuild_in_place True # rebuild my_model.pdb in place # (as opposed to building from scratch) start_chains_list 4 # chain 1 starts at residue 4 # rebuild residues 21-27 of chain "" and 31-42 of chain "" # rebuild_res_start_list 21 31 # rebuild_res_end_list 27 42 # rebuild_chain_list "" "" # n_cycle_rebuild_min 5 # n_cycle_rebuild_max 10 # AutoBuild will run automatically from here on with no more inputs I hope that helps! The new version of PHENIX that will be out very soon fixes many other problems as well! All the best, Tom T At 03:26 AM 3/13/2007, john kryst wrote: >Hi phenixbb !! > > I have few questions. > >1. Is there any utility in phenix to write out pdb formatted (which >is ready to deposit) output file.. like xtal_pdbsubmission utility in CNS. >2. In Autobuild wizard how to ask the program to use the Free R >flags present in the file. It always generates new Free R flags >during refinement. >One general question. > >Does the rmsd estimation (for eg. rmsd_bonds ) depends on the >program we use ?? > >I have been refining in CNS. then i used Autobuild wizard to build >my model. when i went back to cns the rmsd of bond increased ( >0.0218 A). But phenix.refine says it it 0.007A. > >Thanks in advance for your kind inputs. > >regards >john >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Re: [phenixbb] phenix.refine problems with my pdb
by Nicholas Noinaj 16 Mar '07

16 Mar '07

matt, can't offer much help, but have you tried to remove the ligand and try refinement? it would let you know if the pdb file or the presence of the ligand is the problem. at least let you would know where you should focus your attention. if all else fails, have you tried getting parameters for your ligand from the PRODRG Server and using that for inputing the ligand parameters into phenix.refine directly when you setup the refinement job? (I think i have done this before???) here is the website in case you aren't familiar... http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Again, Best of luck! cheers, nick -----Original Message----- From: Matthew Bowler <mwb(a)mrc-dunn.cam.ac.uk> To: phenixbb(a)phenix-online.org Date: Thu, 15 Mar 2007 13:00:42 +0000 Subject: [phenixbb] phenix.refine problems with my pdb Dear All, I am trying to run phenix.refine but I keep getting the message: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 308 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions. Note that elbow.builder is available to create restraint definitions. I have run my ligands through elbow and used the output .cif but I still get the same message. I can find no info on this problem in the manual or the BB, can anyone help? Thanks in advance, yours, Matt. Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] phenix.refine problems with my pdb
by Nicholas Noinaj 15 Mar '07

15 Mar '07

matt, >>> Number of atoms with unknown nonbonded energy type symbols: 308 just curious, did you have 308 waters? as peter said, hard to determine exact problem without some files or examples to look at. also phenix does a good job with water picking, in my little experience. just one more question, when you do get the refinement to work, is your ligand(s) included with the protein model? just no waters, right? it wasn't completely clear from your message. if the ligands aren't included, i recommend adding it(them) back and see if refinement works. then if that works, try water picking within phenix. again, best of luck. cheers, nick -----Original Message----- From: Matthew Bowler <mwb(a)mrc-dunn.cam.ac.uk> To: noinaj(a)uky.edu, PHENIX user mailing list <phenixbb(a)phenix-online.org> Date: Thu, 15 Mar 2007 14:15:45 +0000 Subject: Re: [phenixbb] phenix.refine problems with my pdb Thanks for replies so far.... I removed all ligands and then waters - the waters seem to be the problem as the protein model is now refining, do they need to be treated/marked in a different way for phenix? Thanks again, Matt. On 15 Mar 2007, at 13:32, Nicholas Noinaj wrote: > matt, > > can't offer much help, but have you tried to remove the ligand and > try refinement? it would let you know if the pdb file or the > presence of the ligand is the problem. at least let you would know > where you should focus your attention. > > if all else fails, have you tried getting parameters for your > ligand from the PRODRG Server and using that for inputing the > ligand parameters into phenix.refine directly when you setup the > refinement job? (I think i have done this before???) > > here is the website in case you aren't familiar... > http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ > > Again, Best of luck! > > > > cheers, > nick > > > -----Original Message----- > From: Matthew Bowler <mwb(a)mrc-dunn.cam.ac.uk> > To: phenixbb(a)phenix-online.org > Date: Thu, 15 Mar 2007 13:00:42 +0000 > Subject: [phenixbb] phenix.refine problems with my pdb > > Dear All, > I am trying to run phenix.refine but I keep getting the message: > > > Sorry: Fatal problems interpreting PDB file: > Number of atoms with unknown nonbonded energy type symbols: 308 > Please edit the PDB file to resolve the problems and/or supply a > CIF file with matching restraint definitions. Note that > elbow.builder is available to create restraint definitions. > > I have run my ligands through elbow and used the output .cif but I > still get the same message. I can find no info on this problem in > the manual or the BB, can anyone help? Thanks in advance, yours, > Matt. > > > > > > Matthew Bowler > MRC Dunn Human Nutrition Unit > Wellcome Trust / MRC Building > Hills Road > Cambridge CB2 2XY > Tel: 0044 (0) 1223 252826 > Fax: 0044 (0) 1223 252825 > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825

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Few questions
by john kryst 15 Mar '07

15 Mar '07

Hi phenixbb !! I have few questions. 1. Is there any utility in phenix to write out pdb formatted (which is ready to deposit) output file.. like xtal_pdbsubmission utility in CNS. 2. In Autobuild wizard how to ask the program to use the Free R flags present in the file. It always generates new Free R flags during refinement. One general question. Does the rmsd estimation (for eg. rmsd_bonds ) depends on the program we use ?? I have been refining in CNS. then i used Autobuild wizard to build my model. when i went back to cns the rmsd of bond increased (0.0218 A). But phenix.refine says it it 0.007A. Thanks in advance for your kind inputs. regards john

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phenix.refine problems with my pdb
by Matthew Bowler 15 Mar '07

15 Mar '07

Dear All, I am trying to run phenix.refine but I keep getting the message: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 308 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions. Note that elbow.builder is available to create restraint definitions. I have run my ligands through elbow and used the output .cif but I still get the same message. I can find no info on this problem in the manual or the BB, can anyone help? Thanks in advance, yours, Matt. Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825

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Two groups per residue and multiple trajectories for simulated annealing
by Stephen Graham 03 Mar '07

03 Mar '07

Hi all, I am taking my first tentative steps into the world of phenix.refine with a somewhat problematic 3 A data set and I had a few questions that Google couldn't answer. I am running phenix.refine version 1.24.1b (intel-linux-2.6) from the command line. Firstly, is it possible to do 'grouped' adp refinement with 2 groups per residue (like the good old bgroup.inp of CNS)? Secondly, is it possible to specify multiple starting trajectories for simulated annealing? I often find it handy to do 10 runs of simulated annealing and overlay the output co-ordinates to see where the 'wobbly' bits are. Lastly, can the latest version of phenix.refine do SA omit maps? Thanks, Stephen P.S. My .def file is the default (from phenix.refine --dry-run) w/ the following changes: 86,87c86,87 < refine_adp_individual = True < refine_adp_group = False --- > refine_adp_individual = False > refine_adp_group = True 92c92 < simulated_annealing = False --- > simulated_annealing = True -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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