August 2007 - phenixbb - phenix-online.org

Question about antibumping restraints and restraints on dihedrals
by Madhumati Sevvana; Biotechnik 22 Aug '07

22 Aug '07

Hi! I could successfully refine a merohedral twin in phenix.refine but I have a few unanswered questions: 1. Is there a way of applying antibumping restraints to decrease the number of clashes in phenix.refine, I looked at older posts but couldn't get a satisfactory guideline regarding the same. 2. The default setttings for geometry refinement looks like this: refinement.geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } Do I have to change "dihedrals=True" if I do not want to put restraints on dihedrals. I was thinking that one puts restraints on psi/phi angles only by setting "discard_psi_phi = False" because when I set it to "discard_psi_phi = True", the Ramachandran plot was much better. But I did not want to do this because then the Ramachandran plot is no more a validation tool. I just wanted to know if Unknowingly I did that by setting up "dihedrals = None". Thank you in advance. Regards, Madhu. ------------------------------------------ Madhumati Sevvana, PhD Lehrstuhl fuer Biotechnik Friedrich-Alexander-Universitaet Henkestr. 91, D-91052 Erlangen, Germany Tel: 0049-9131-8523083 Email: msevvana(a)biologie.uni-erlangen.de -------------------------------------------

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Re: [phenixbb] low res structures and Phenix
by Tom Terwilliger 21 Aug '07

21 Aug '07

Hi John, I'll answer the first of your questions... -Tom T >I have a couple of questions regarding low res structures in Phenix >(about 3.5 angstroms res). > >1. Can Phenix do B-factor sharpening for improved maps? If not >what program do people usually use for this? If you are using the AutoSol wizard, you can use the keywords: correct_aniso=True b_overall=20.0 to force correction of any anisotropy in your data and to set the overall B to 20.0. Note that this will affect all the maps produced by the AutoSol wizard. I have not yet found this to improve the quality of the resulting model; if it works for you please let me know! You can also use phenix.xtriage to do this: phenix.xtriage perfect.mtz hklout=output.mtz aniso.action=True aniso.final_b=user_b_iso aniso.b_iso=77 will set the b_iso of perfect.mtz to 77 >2. How can one optimize Ksol and Rprobe (bulk solvent model) in Phenix? > >3. Are there any other suggestions for dealing with low resolution >structures in Phenix? > >Thanks, >John Bruning >_______________________________________________ >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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cis peptide and pdb head
by Jianghai Zhu 21 Aug '07

21 Aug '07

Hi, How does phenix.refine treat cis peptide? Will it automatically detect it and restrain it like refmac5? or do I have to input the information somewhere? or generally how does phenix.refine treat the pdb head? I remember that some earlier version manual stated that all the head information are discarded, is that correct? Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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low res structures and Phenix
by John Bruning 21 Aug '07

21 Aug '07

Hi, I have a couple of questions regarding low res structures in Phenix (about 3.5 angstroms res). 1. Can Phenix do B-factor sharpening for improved maps? If not what program do people usually use for this? 2. How can one optimize Ksol and Rprobe (bulk solvent model) in Phenix? 3. Are there any other suggestions for dealing with low resolution structures in Phenix? Thanks, John Bruning

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Re: [phenixbb] autobuild wizard question
by Tom Terwilliger 19 Aug '07

19 Aug '07

Hi Jeff, I'm sorry for the trouble with the AutoBuild Wizard! I was not able to duplicate the problem with my version and putting in a model with 2 chains and trying to do rebuild_in_place of just a few residues, unfortunately. Everything seemed to work as it is supposed to. Can you check a couple things: 1. Make sure you have the latest version of PHENIX (development version) from the website. 2. Make sure that the range of residues you want to rebuild is at least 2 in from each end of the chain (so if the chain is 1-350, you can rebuild 3-6 or 347-348 but not 340-350). 3. If you accidentally give the Wizard a range that is too big, it should give you an error message and stop, but if you fix the range then it should go on. 4. Try running the Wizard from the command line, and specify "verbose=True debug=True" which will help because it gives you a lot of output that may help figure out what is going on. You will need to add also " |tee debug.log" to catch the output from this run. If none of those things help, then if you can send me the AutoBuild_run_xx_.output file from your GUI-version run and the output from running from the command line; that may help me figure out what is going wrong. Thanks! -Tom T Jeff Habel wrote: >Im a new PHENIX user and having trouble with the Autobuild wizard. > >The structure has 2 molecules in the asymmetric >unit and I am trying to build a small portion >(286-297) of both chains. I have tried building >both at the same time and trying just chain A >but always receive the error about needing 2 >amino acids on either end for anchoring the >build. Every time I alter the build range (284 >299 282 301 etc) the error persists. > >Any suggestions would be appreciated. > >Thanks, > >-Jeff 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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New CCI Apps
by Ralf W. Grosse-Kunstleve 19 Aug '07

19 Aug '07

On behalf of the Phenix development team I'm pleased to announce the release of a new CCI Apps version: http://phenix-online.org/download/cci_apps/ Send bug reports to: bugs(a)phenix-online.org For help write to: help(a)phenix-online.org Version 2007_08_18_1856 phenix.reduce updated to produce PDB-V3 hydrogen names (Duke group) phenix.refine updated to handle the new atom names from the remediated PDB-V3. Currently protein and RNA/DNA only. For ligands with new names, use elbow.builder to generate CIF files with matching restraints. phenix.refine manual significantly re-worked phenix.refine bug fixes: - Proper handling of chain breaks, to avoid incorrect angle, dihedral, chirality and planarity restraints. This bug was likely to lead to bad restraints for structures with alternative conformations. - Avoid Wilson B crash for no data if low resolution omitted - Proper handling of NCS + remove_h=true - Proper handling of negative residue numbers - Avoid segfault in twin refinement - Cumulative fixes and enhancements in picking and refinement of interatomic scatterers (IAS) phenix.refine vdw_1_4_factor changed from 2/3 to 0.8 (to improve geometry and MolProbity clash scores in particular) phenix.refine obsolete remove_hydrogens option removed New phenix.pdbtools (use --help) Command aliases removed (i.e. mmtbx.xtriage is now only available as phenix.xtriage) Most major commands renamed to phenix.*, e.g. iotbx.emma -> phenix.emma iotbx.pdb.hierarchy -> phenix.pdb.hierarchy Use phenix<TAB> (in most shells) to get a full list of available phenix commands. eLBOW - Perform simple eLBOW jobs in COOT - Automatically perform the appropriate calculations on all the unknown ligands in a PDB file and combine the CIF results into one file - Covalent bonding of ligands to macromolecules (phase I implementation) - Print the sequence of PDB file (elbow.print_sequence) - User control of addition and writing of Hydrogens - Output of TRIPOS mol2 files - User control over naming of output files - elbow.join_cif_files has re-ordered arguments (target as last argument) - elbow.link_edits will generate "edits" from PDB LINK records for input to phenix.refine - elbow.metal_coordination will generate phenix.refine "edits" for metal coordination spheres including angles

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autobuild wizard question
by Jeff Habel 17 Aug '07

17 Aug '07

I'm a new PHENIX user and having trouble with the Autobuild wizard. The structure has 2 molecules in the asymmetric unit and I am trying to build a small portion (286-297) of both chains. I have tried building both at the same time and trying just chain A but always receive the error about needing 2 amino acids on either end for anchoring the build. Every time I alter the build range (284... 299... 282... 301... etc) the error persists. Any suggestions would be appreciated. Thanks, -Jeff **************************************** Jeff Habel PhD Scripps Florida Drug Discovery 5353 Parkside Dr, RF-1 Rm 102 Jupiter, FL 33458 Phone: 561-799-8849 Fax: 561-799-8957 Email: jhabel(a)scripps.edu *****************************************

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Re: [phenixbb] TLS refinement
by Pavel Afonine 17 Aug '07

17 Aug '07

Hi John, > I was wondering if there is an easy way to take the output from TLSmd > and input the definitions into phenix.refine. Unfortunately, I do not know since it never happened to me to use it. It is our long term plan to implement our own automatic TLS domains identification option. > If any one has an example file of a phenix TLS file with multiple TLS > definitions per chain I would love to have it (The manual just gives > an example of TLS definitions of one per chain, but I am getting > confused on how to define mutlitple). I'm loading two files at the web address below: one with TLS selections for multiple groups, another one is the PDB file with refined model and TLS records in its header. This is actually the most complex selection for TLS groups I ever used -:) http://cci.lbl.gov/~afonine/tls_selections/ Please let me know if you have any more questions. Pavel.

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TLS refinement
by John Bruning 17 Aug '07

17 Aug '07

Hi, I was wondering if there is an easy way to take the output from TLSmd and input the definitions into phenix.refine. If any one has an example file of a phenix TLS file with multiple TLS definitions per chain I would love to have it (The manual just gives an example of TLS definitions of one per chain, but I am getting confused on how to define mutlitple). Thanks, John Bruning

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Re: [phenixbb] Question about precedence of command line parameters vs. .def file
by Ralf W. Grosse-Kunstleve 14 Aug '07

14 Aug '07

Hi Carsten, > I see how the loading of both pdb files can be a desired feature, but I > also recall reading somewhere that command line params take precedence > over .def files, which in turn takes precedence over defaults. There > seems to be some deviation from that philosophy. Each parameter has a bunch of associated attributes to control the behavior. The attribute that causes trouble here is .multiple=True. It means that you can specify multiple values. Values accumulate in the order given. .multiple=True is used in many places and in general this feature works well, but in the case of the pdb file name it sometimes causes confusion. Unfortunately I don't see an obvious way around this. It would be possible to support something like pdb.file_name==your.pdb, where == means discard all accumulated values and start over with the new value, but that wouldn't be very intuitive. Or we'd have to stop supporting reading of multiple pdb files. I wonder if you could achieve your goals with a different approach. The idea is not to use the .def files produced by phenix.refine. I'm guessing you're doing this because they contain all your accumulated customizations defined via the command line. Could you organize your workflow to accumulate the customizations in a separate file, then pass that file as another argument? E.g.: Content of "params" file: refinement.main.macro_cycles=5 refinement.main.high_resolution=3 phenix.refine my.pdb params > This also would help future automation we are implementing, because > it would eliminate the need to read and parse an existing .def. file. Parsing and rewriting a .def file is very easy from Python. If you have phenix, you also have both Python and a parameter file parser and writer. The "phil" parser/writer is documented in this newsletter article: http://cci.lbl.gov/publications/download/iucrcompcomm_jan2005.pdf I could help you getting started if that's an interesting alternative. If you can think of a more intuitive way of handling the interaction of parameters with multiple values and command-line parameters, please let me know! Ralf

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