- phenixbb - phenix-online.org

Re: [phenixbb] selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Thanks to all who replied. And thank you Ralf for your suggestion (quoted below), this worked very nicely! Somehow I missed this possibility in the online documentation. To reply to Pavel's question regarding how I figured out that tris is present at 1/2 occupancy: (1) density was first modelled with waters but they were too close together, and there was a fairly clear tetrahedral shape. (2) phosphate didn't refine well -- lead to huge negative difference peak at the P atom. (3) only other tetrahedral shape molecule in the soup was tris (TAM), and after refining just the tetrahedral core it was possible to see where the three arms extended. (4) b-factors for the tris were high relative surrounding protein atoms, and extraneous density suggested two alternate conformations for the nearby arg side-chain, one of which is too close to realistically exist next to the tris ligand. the other clue was that trial occupancy refinement of all atoms put most tris atoms in the 0.4-0.6 occupancy range. (5) tris with 0.5 occupancy, arg with two alt confs, plus a few waters at 0.5 occupancy is so far the best model with no significant different densities for this region. (6) the modelling will need to be confirmed with an SA omit ... > Hi Cathy, > > > The density suggests that when tris is not there, > > a side chain moves very close to that position > > You could model this with alternative conformations. If you assign > "altloc" A and B to two conformers of your protein, and just, say, B > to your TAM, then the ligand would only "see" your B protein. If you > don't define the B conformer (no atoms) then TAM wouldn't see that > part of the protein at all. > Actually, this approach seems better to me than working with > atom selections. > > Ralf

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Re: [phenixbb] selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Hi Ralf, That is disappointing. Lovely maps produced after a few phenix.refine runs for a 1.6 A structure revealed an unexpected tris ligand (TAM) with occupancy ~0.5. The density suggests that when tris is not there, a side chain moves very close to that position, thus my question. In other regards phenix seems a great step forward in automating refinement, and I look forward to new developments. best wishes, Cathy > Hi Cathy, > > > Is it possible to turn off nonbonded restraints for particular > > residues/monomers, or for atoms with occupancy less than 1.0? > > Nope, sorry. It is on the (long) to-do list. > BTW: each time someone asks the priority goes up. > > Ralf

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selective nonbonded restraint removal
by Cathy Lawson 04 Sep '07

04 Sep '07

Hi Phenix bber's, I have been trying out phenix.refine and like it very much so far. Is it possible to turn off nonbonded restraints for particular residues/monomers, or for atoms with occupancy less than 1.0? Thanks, Cathy Lawson /////////////////////////////////////////////////////// http://rutchem.rutgers.edu/~lawson

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SAD related query
by tara kashav 04 Sep '07

04 Sep '07

Dear all, I am a novice user of phenix. I am trying to obtain phases for SAD dataset collected at 2.5 angs from autosol.But when i give the phases to autobuild, the R-factor is not decreasing below 49%. Also, in warp, it is unable to built with a message "encounterd an unknown element". Can someone suggest me what could be the problem. Thanks for any suggestion in advance. Tara Kashav On 9/3/07, phenixbb-request(a)phenix-online.org < phenixbb-request(a)phenix-online.org> wrote: > > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. command-line Patterson maps (Bryan W. Lepore) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 2 Sep 2007 00:07:51 -0500 (CDT) > From: "Bryan W. Lepore" <bryanlepore(a)mail.utexas.edu> > Subject: [phenixbb] command-line Patterson maps > To: phenixbb(a)phenix-online.org > Message-ID: > < > Pine.LNX.4.64.0709020001190.16588(a)cpe-70-116-17-26.austin.res.rr.com> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > will phenix calculate Pattersons from trial sites or a reflection file on > the command line? i.e. something besides hacking what is already there. > > e.g. cns has predict_patterson.inp. i can't seem to find a way to do it > from the command line - such as `phenix.patterson --sg=94 > reflections.mtz`. i saw phenix.maps but that looks like electron density > only. > > -bryan > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 22, Issue 1 > *************************************** > -- Tara Kashav, Dr. S. Gourinath's Lab, Lab No 430, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067

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command-line Patterson maps
by Bryan W. Lepore 04 Sep '07

04 Sep '07

will phenix calculate Pattersons from trial sites or a reflection file on the command line? i.e. something besides hacking what is already there. e.g. cns has predict_patterson.inp. i can't seem to find a way to do it from the command line - such as `phenix.patterson --sg=94 reflections.mtz`. i saw phenix.maps but that looks like electron density only. -bryan

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ligand restraints
by Jeff Habel 30 Aug '07

30 Aug '07

I have a ligand with two phenyl rings where 2Fo and difference density clearly shows some torsion angle between the two rings. However, no matter how many times I tilt one ring refinement always makes them coplanar. Is there an option that I can use in phenix.refine to prevent the co-planarity or how do people typically handle this situation? Thanks for the help. All the best, -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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Turing off Auto-Modify initial isotropic ADP
by James Fraser 30 Aug '07

30 Aug '07

I'm trying to do an Fcalc with "main.number_of_macro_cycles=0 main.bulk_solvent_and_scale=false export_final_f_model=mtz ", but the b-factors get randomized before the 0th cycle of refinement (see excerpt from log below). Is there anyway to turn this off? Thanks, jf <<LOG FILE>> ----------Auto-Modify initial isotropic ADP---------- Randomizing |-ADP statistics (Wilson B = -4.823)------------------------------------------| .... -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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occupancy refinement question
by John Bruning 27 Aug '07

27 Aug '07

Hi, I have a ligand with dual conformations. I want to do group occupancy refinement on the conformers (each conformer is one group). I keep having trouble. The ligand is one chain named chain E and conformer 1 has residue name ADRG and conformer 2 has residue name BDRG. This is what I suppose my .def file should have in it: occupancies { individual = None group = "chain E and resname ADRG" group = "chain E and resname BDRG" one_occupancy_group_per_residue = True } When I run this it tells me I have an ambiguous selection. Any ideas why this isn't working and how I can change my .def file to make it work?

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Re: [phenixbb] occupancy refinement question
by Paul Adams 27 Aug '07

27 Aug '07

Hi is it possible that the A and B in the residue name are the alternate conformation ids? If so your selection should use the DRG resname and the altloc to select the appropriate residues. Paul Adams Lawrence Berkeley Laboratory -----Original Message----- From: John Bruning <jbruning(a)gmail.com> Date: Monday, Aug 27, 2007 1:38 pm Subject: [phenixbb] occupancy refinement question To: phenixbb(a)phenix-online.orgReply-to: PHENIX user mailing list <phenixbb(a)phenix-online.org> Hi, > >I have a ligand with dual conformations. I want to do group occupancy refinement on the conformers (each conformer is one group). I keep >having trouble. The ligand is one chain named chain E and conformer 1 has residue name ADRG and conformer 2 has residue name BDRG. This is what I suppose my .def file should have in it: > >occupancies { > individual = None > group = "chain E and resname ADRG" > group = "chain E and resname BDRG" > one_occupancy_group_per_residue = True > } > >When I run this it tells me I have an ambiguous selection. > >Any ideas why this isn't working and how I can change my .def file to make it work? >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb >

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PX Jobs Team Leader, Postdoc, Tech (SGC-Oxford).txt
by Frank von Delft 24 Aug '07

24 Aug '07

My group has several vacancies to fill immediately: a Team Leader for Infrastructure and Methods Development; two postdoc positions; and a technician. This is the Protein Crystallography group of the Structural Genomics Consortium, Oxford. For details, please see respectively: Team Leader: http://www.sgc.ox.ac.uk/jobs/07057.html Postdocs: http://www.sgc.ox.ac.uk/jobs/07058.html Technician: http://www.sgc.ox.ac.uk/jobs/07067.html Feel free to contact me for details. The remit of the Structural Genomics Consortium (SGC) is to solve human proteins of medical relevance and place them in the public domain without restrictions; it is funded by a consortium of public and industrial funders, and has independently operating sites in Oxford and Toronto Universities and Karolinska Institutet (Stockholm). The Oxford site solved nearly 200 such structures in its first three years, and has now entered Phase II, with 4 years of funding till June 2011; it now has an increased emphasis on chemical biology and membrane proteins. The Protein Crystallography group collaborates tightly with the 5 other groups to get their purified proteins crystallized and solved -- five per month, to be precise. As importantly, with all the robotics and toys you'd care for, and access not only to stacks of real, interesting samples but also to heaps of structured data accumulated during Phase I, we're ideally positioned for development and testing of crystallographic methods, which will be the major scientific thrust of the group in this phase. Enthusiastic crystallographers, especially those that really enjoy the nuts and bolts of the technique and mucking around with tricks and toys, both crystallization and algorithms, are encouraged to apply. phx.

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Help making selections
by James Fraser 23 Aug '07

23 Aug '07

I am trying to refine a structure where I want chains C and D refined anisotropically. Chain A refined isotropically and as a TLS group. Chain B refined isotropically and as a (separate) TLS group. Chain S (waters) just refined isotropically. I've tried playing around with selections on the command line and in the .def file. Yet always end up not getting the refinement to run correctly or have phenix.refine throw an "AssertionError". I'm using the latest CCIapps phenix.refine. Can someone help me out. Below are the excerpt from the DEF file and the error message thrown to the screen. Thanks, James --FROM DEF FILE-- refine { strategy = *individual_sites rigid_body *individual_adp group_adp *tls \ individual_occupancies group_occupancies group_anomalous none sites { individual = None rigid_body = None } adp { individual { isotropic = None anisotropic = "chain c or chain d" } group = None one_adp_group_per_residue = True tls = "chain a" tls = "chain b" } occupancies { individual = None group = None one_occupancy_group_per_residue = False } anomalous_s --FROM LOG FILE-- ----------Target weights (before refinement)---------- Traceback (most recent call last): File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in ? command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 80, in run refine_object.run( File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1244, in run log = log) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 268, in refinement_machine log = log) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py", line 137, in __init__ compute_gradients = True) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/mmtbx/mmtbx/restraints.py", line 126, in energies_adp_aniso xray_structure = xray_structure, File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", line 113, in __init__ self.check_flags(fl_i) File "/programs/cci_apps_2007_08_18_1856/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", line 181, in check_flags assert not fl.use_u_aniso() AssertionError -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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Re: [phenixbb] density modification?
by Tom Terwilliger 23 Aug '07

23 Aug '07

Hi John, Yes, you have several choices for density modification in phenix: 1. Use your experimental Fobs and phases as a starting point for the AutoBuild Wizard. After the first cycle, you will have density-modified phases. In this example below model-building is turned off with maps_only=True to make this go quickly: phenix.autobuild my_fobs_exptl_phases.mtz input_seq_file=seq.dat \ maps_only=True \ n_cycle_build_max=1 n_cycle_rebuild_max=0 Your density-modified phases will be in AutoBuild_run_1_/overall_best_denmod_map_coeffs.mtz after this run. 2. You can also use resolve directly in phenix with a command like this phenix.resolve<<EOD hklin my_fobs_exptl_phases.mtz labin FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD no_build solvent_content 0.45 EOD Either of these will do solvent flattening and histogram matching. If you have ncs you can specify it with a set of matrices or with a set of heavy-atom positions in a PDB file that show the NCS with: ha_file heavy_atoms_with_ncs.pdb All the best, Tom T . 03:26 PM 8/22/2007, you wrote: >Is there a way to do density modification in Phenix (solvent and or >histogram)? If so how? > >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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density modification?
by John Bruning 22 Aug '07

22 Aug '07

Is there a way to do density modification in Phenix (solvent and or histogram)? If so how? Thanks, John Bruning

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Re: [phenixbb] Question about antibumping restraints and restraints on dihedrals
by Ralf W. Grosse-Kunstleve 22 Aug '07

22 Aug '07

Hi Madhu, > 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. The antibumping restraints (nonbonded interactions) are on by default. Currently there isn't a syntax to turn them off or to change the default parameterization. If you refine for a few cycles with the weight for the x-ray target set to zero (wxc_scale=0) the clashes should definitely go away. Then go back to normal refinement (wxc_scale=0.5). I'd hope that the clashes don't come back. Otherwise that's what the x-ray data guide the minimization to, even though the restraints are pushing back. > 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" This will not work: Sorry: Invalid atom selection: refinement.geometry_restraints.remove.dihedrals="True" (RuntimeError: Syntax error.) You have to specify atom selections to *remove* default restraints. > 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". No, if you leave the geometry_restraints.remove block untouched you'll get all restraints incl. dihedrals, except for the peptide psi and phi angles, which are controlled by the dedicated parameter you quote. Cheers, Ralf

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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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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

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