- phenixbb - phenix-online.org

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

2 1

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

1 0

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

1 0

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 *****************************************

1 0

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.

1 0

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

2 1

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

1 0

Question about precedence of command line parameters vs. .def file
by Schubert, Carsten [PRDUS] 14 Aug '07

14 Aug '07

Hi, I have a question / request about parameters defined on the command line vs. defined in the .def file are handled. Specifically the input.pdb.file_name parameter. I noticed that if I have already a input.pdb.file_name defined in the .def file and call phenix.refine with another pdb file, both files are loaded. If both pdb files represent the same protein in different stages of refinement that obviously causes the job to fail due to close non-bonding interactions. 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. For me this is more a work-flow issue (which becomes important if one does to many structures per day ...) than a bug. I'd really like to minimize the time spend on editing the def file and just define new job parameters from the command line and have the def file fill in the missing bits. This also would help future automation we are implementing, because it would eliminate the need to read and parse an existing .def. file. There are ways around this but not as clean, but that is another matter .... Would it be possible to implement a switch which would check for duplicate parameters on the command line vs. .def file, give precedence to the command line and run the job like that? That way we would not break the existing scheme, which other people may have already grown accustomed too. Other suggestions are welcome too. Cheers, Carsten

2 1

conversion from h3 to r3 with phenix apps
by Green, Todd 14 Aug '07

14 Aug '07

Hello all, I have what i believe to be a rhombohedral crystal that has an insanely large cell with the hexagonal setting: 533.026 533.026 652.887 90.000 90.000 120.000 and a modestly large cell comparatively with the rhombohedral setting: 377 377 377 90 90 90 I should be able to easily reindex to the smaller cell in scalepack but for some reason i'm not getting it to work correctly. Rather than struggle further on a friday afternoon, i figured that i'd give a phenix app a try. i assume xtriage can do this, can someone point me in the correct direction? thanks in advance- Todd

3 7

refinement questions
by Sudharsan Sridharan 10 Aug '07

10 Aug '07

Hi all, I'm starting to refine a structure using phenix.refine. Almost all my model residues have been built starting from a Sharp map. I've been trying phenix.refine with and without SA and getting bond angle rmsds of 1.0 -1.1 (2.5 A data, using mlhl targets; example below) (yet to add water and also trying water picking in phenix.refine). I'm wondering if this sounds low (I have read discussions on bond and angle rmsds). More importantly I'd like to know how to work with different parameters (weights etc) during refinement in phenix. Could you please point to what params are safe to manipulate. Thanks, Sid. REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS ******************* REMARK Start: r_work = 0.3637 r_free = 0.4003 bonds = 0.010 angles = 1.175 REMARK Final: r_work = 0.2607 r_free = 0.3236 bonds = 0.007 angles = 1.017 REMARK ************************************************************************

2 1