- 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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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

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

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Position for PSI Knowledgebase development
by Paul Adams 08 Aug '07

08 Aug '07

======================================================================= Lawrence Berkeley National Laboratory Software Developer II ======================================================================= Software Developer II Job ID: 20930 Division: Physical Biosciences Date Opened: 8/7/2007 Summary This position will be part of the Computational Crystallography Initiative at Lawrence Berkeley Lab and will be responsible for developing a web site to disseminate information about the Technologies developed by the NIH Protein Structure Initiative (PSI). This program funds the majority of structural genomics efforts within the US and is responsible for the development of many new technologies that are useful to macromolecular crystallographers. This technology resource is part of the larger PSI Knowledge Base that will provide an information portal for the scientific community. Duties Essential: Under general direction of the Principal Investigator: Develop and maintain web site documenting PSI developed technologies. Interact with PSI researchers to collect information about new technologies. Create a relational database to store crystallographic data. Install and maintain SVN repositories for the PSI community. Marginal: Perform routine analysis of crystallographic data. Maintain web site computing hardware and software. Other duties as assigned. Qualifications Essential: Experience with writing and maintaining HTML web pages. Knowledge of standard programming methods, and Python in a UNIX environment. Strong analytical and organizational skills. Ability to handle multiple tasks in parallel. Excellent interpersonal skills for working in a diverse team environment, ability to interact effectively with other scientists, and to address their needs in an effective and timely manner. Marginal: B.S. Degree or higher in biophysics, computer science, chemistry, electrical engineering, physics or related field preferred or equivalent experience, with demonstrated programming experience. Experience maintaining computing hardware and software. Experience with analysis of crystallographic data. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20930. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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ncs restraints weight
by Daniele de Sanctis 06 Aug '07

06 Aug '07

Dear all, i'm refining a low resolution structure (3.2A) with four molecules in the asymmetric unit. I saw that phenix.refine doesn't allow constraints, so i'd like to change the restraints weight but i can't find the right keyword... thanks for your help d -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartato 127 2781-901 Oeiras Portugal

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Re: [phenixbb] set_biso_to_wilson_b gone?
by Pavel Afonine 06 Aug '07

06 Aug '07

Hi Luca, > I've just noticed that in the last version of PHENIX (1.3b-d7) this is > not recognised anymore: > > refinement.modify_start_model.adp.set_biso_to_wilson_b = true > > is this intentional? I'm afraid, yes. There are some technical reasons for this. You still have at least two ways of doing this: 1) When running phenix.refine : % phenix.refine data.mtz model.pdb modify_start_model.adp.set_b_iso=xxx where xxx is Wilson B values (that you may get from previous phenix.refine runs; phenix.refine reports it). 2) We recently added a tool for PDB file(s) manipulations. Currently it is very simple but will grow based on needs and user's requests. For example, it can read in a model and for selected or all atoms: - modify ADP (randomize, shift, set to a value, scale, convert to/from iso(aniso)tropic); - modify sites (shake, apply rotation / translation); - modify occupancies; - remove selected atoms; - write out a PDB file with modified model. To get started type: phenix.pdbtools -h I'm attaching a copy of a quick manual for phenix.pdbtools (it will be a part of new updated PHENIX documentation). Pavel.

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Re: [phenixbb] Problematic dataset
by Peter Zwart 05 Aug '07

05 Aug '07

Hi Lucas, Your P21 just looks twinned. Have a look at the last section of the xtriage output: ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - <I^2>/<I>^2 : 1.915 - <F>^2/<F^2> : 0.821 - <|E^2-1|> : 0.677 - <|L|>, <L^2>: 0.442, 0.267 Multivariate Z score L-test: 3.623 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | h,-k,-h-l | PM | 0.090 | 0.406 | 0.417 | 0.370 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 6.379 (correpsonding p value : 6.273e-01) The largest off-origin peak in the Patterson function is 6.38% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are twin laws possible given the crystal symmetry, twinning could be the reason for the departure of the intensity statistics from normality. It might be worthwhile carrying out refinement with a twin specific target function. ------------------------------------------------------------------------------- You might have NCS parallel to the twin axis. If you run mmtbx.xtwin_map_utils on your P21 data, you get a mtzfile called obs_and_calc.mtz push that through xtriage (make sure to specify labels for observed and calculated data) to get the RvsR statistic. When you do that, please also provide the keyword 'perform=True' on the xtriage command line for my pleasure and send me the resulting log file. I guess the twin refinement will push the r values down a bit. Note that for futurte reference, xtriage produces a logfile as well, usually named logfile.log unless you ask it to be a different name. logfile.log contains some ccp4 style graphs you can view with loggraph (such as the L, NZ, Britton and H curves). If the above is too cryptic and you need more info, please let me know. HTH Peter Lucas Bleicher wrote: > Hi, Peter! > > I am sending the xtriage output for both space groups. > > So, the correct approach would be to use the MTZ > processed in P21 with the twin law from the xtriage > output from this MTZ file? > > Thanks in advance, > Lucas > > > Alertas do Yahoo! Mail em seu celular. Saiba mais em http://br.mobile.yahoo.com/mailalertas/ > ------------------------------------------------------------------------ > > ############################################################# > ## mmtbx.xtriage ## > ## ## > ## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ## > ## ## > ############################################################# > Date 2007-07-31 Time 16:43:49 BRT -0300 > > > ##-------------------------------------------## > ## WARNING: ## > ## Number of residues unspecified ## > ##-------------------------------------------## > > > Effective parameters: > scaling.input { > parameters { > asu_contents { > n_residues = None > n_bases = None > n_copies_per_asu = None > } > misc_twin_parameters { > missing_symmetry { > tanh_location = 0.08 > tanh_slope = 50 > } > twinning_with_ncs { > perform_analyses = False > n_bins = 7 > } > twin_test_cuts { > low_resolution = 10 > high_resolution = None > isigi_cut = 3 > completeness_cut = 0.85 > } > } > reporting { > verbose = 1 > log = "logfile.log" > ccp4_style_graphs = True > } > } > xray_data { > file_name = "LamNatP1High_scala1.mtz" > obs_labels = "MEAN_lnls,SIGIMEAN_lnls" > calc_labels = None > unit_cell = 52.16379929 64.59190369 108.2256012 89.99259949 89.99089813 \ > 66.10500336 > space_group = "P 1" > high_resolution = None > low_resolution = None > } > } > <scitbx_array_family_flex_ext.double object at 0xb5e96dac> > > > Symmetry, cell and reflection file content summary > > Miller array info: LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls > Observation type: xray.amplitude > Type of data: double, size=94082 > Type of sigmas: double, size=94082 > Number of Miller indices: 94082 > Anomalous flag: False > Unit cell: (52.1638, 64.5919, 108.226, 89.9926, 89.9909, 66.105) > Space group: P 1 (No. 1) > Systematic absences: 0 > Centric reflections: 0 > Resolution range: 26.0819 1.85 > Completeness in resolution range: 0.854134 > Completeness with d_max=infinity: 0.853839 > > ##----------------------------------------------------## > ## Basic statistics ## > ##----------------------------------------------------## > > > Matthews coefficient and Solvent content statistics > > Number of residues unknown, assuming 50% solvent content > > ---------------------------------------------------------------- > | Best guess : 1220 residues in the asu | > ---------------------------------------------------------------- > > > Completeness and data strength analyses > > The following table lists the completeness in various resolution > ranges, after applying a I/sigI cut. Miller indices for which > individual I/sigI values are larger than the value specified in > the top row of the table, are retained, while other intensities > are discarded. The resulting completeness profiles are an indication > of the strength of the data. > > ---------------------------------------------------------------------------------------- > | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | > ---------------------------------------------------------------------------------------- > | 26.08 - 4.55 | 97.0% | 96.3% | 95.5% | 93.5% | 87.3% | 80.3% | > | 4.55 - 3.62 | 96.5% | 96.1% | 95.4% | 93.8% | 87.8% | 81.2% | > | 3.62 - 3.16 | 95.7% | 94.5% | 93.2% | 89.4% | 78.1% | 66.3% | > | 3.16 - 2.87 | 93.1% | 90.7% | 87.1% | 79.1% | 60.8% | 44.5% | > | 2.87 - 2.67 | 88.4% | 84.0% | 78.5% | 66.7% | 44.0% | 27.9% | > | 2.67 - 2.51 | 85.5% | 78.6% | 71.1% | 57.7% | 32.6% | 17.9% | > | 2.51 - 2.38 | 82.4% | 74.1% | 65.3% | 49.3% | 24.8% | 12.2% | > | 2.38 - 2.28 | 81.6% | 72.3% | 62.4% | 46.0% | 20.4% | 9.0% | > | 2.28 - 2.19 | 78.5% | 67.6% | 55.1% | 37.2% | 14.8% | 5.7% | > | 2.19 - 2.12 | 75.5% | 61.9% | 49.0% | 30.7% | 9.9% | 3.5% | > | 2.12 - 2.05 | 72.1% | 55.6% | 41.8% | 23.7% | 6.3% | 1.9% | > | 2.05 - 1.99 | 68.6% | 50.2% | 35.8% | 17.9% | 4.1% | 1.0% | > | 1.99 - 1.94 | 63.2% | 42.9% | 28.5% | 13.7% | 3.1% | 0.5% | > | 1.94 - 1.89 | 56.6% | 36.7% | 23.2% | 10.4% | 1.7% | 0.3% | > ---------------------------------------------------------------------------------------- > > The completeness of data for which I/sig(I)>3.00, exceeds 85% for > for resolution ranges lower than 2.87A. > The data is cut at this resolution for the potential twin tests > and intensity statistics. > > > Maximum likelihood isotropic Wilson scaling > ML estimate of overall B value of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > 15.59 A**(-2) > Estimated -log of scale factor of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > -2.45 > > > Maximum likelihood anisotropic Wilson scaling > ML estimate of overall B_cart value of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > 15.61, 1.39, -1.33 > 11.40, 0.27 > 21.10 > Equivalent representation as U_cif: > 0.18, -0.04, -0.02 > 0.14, 0.00 > 0.27 > > ML estimate of -log of scale factor of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls: > -2.45 > Correcting for anisotropy in the data > > Some basic intensity statistics follow. > > > > Low resolution completeness analyses > > The following table shows the completeness > of the data to 5 Angstrom. > unused: - 26.0822 [ 0/38 ] 0.000 > bin 1: 26.0822 - 10.5555 [528/541] 0.976 > bin 2: 10.5555 - 8.4726 [551/564] 0.977 > bin 3: 8.4726 - 7.4299 [530/547] 0.969 > bin 4: 7.4299 - 6.7636 [568/582] 0.976 > bin 5: 6.7636 - 6.2860 [525/540] 0.972 > bin 6: 6.2860 - 5.9200 [547/559] 0.979 > bin 7: 5.9200 - 5.6266 [530/546] 0.971 > bin 8: 5.6266 - 5.3839 [519/532] 0.976 > bin 9: 5.3839 - 5.1783 [568/584] 0.973 > bin 10: 5.1783 - 5.0009 [516/532] 0.970 > unused: 5.0009 - [ 0/0 ] > > > > Mean intensity analyses > Analyses of the mean intensity. > Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. > The following resolution shells are worrisome: > ------------------------------------------------ > | d_spacing | z_score | compl. | <Iobs>/<Iexp> | > ------------------------------------------------ > | 9.993 | 7.15 | 0.97 | 0.426 | > | 8.448 | 7.29 | 0.98 | 0.559 | > | 7.451 | 6.09 | 0.97 | 0.676 | > | 4.303 | 4.64 | 0.97 | 1.223 | > | 3.410 | 4.52 | 0.96 | 1.176 | > | 3.333 | 6.63 | 0.96 | 1.262 | > | 3.261 | 5.36 | 0.96 | 1.205 | > | 3.194 | 5.48 | 0.96 | 1.203 | > | 3.071 | 4.87 | 0.94 | 1.183 | > | 2.962 | 6.43 | 0.94 | 1.245 | > | 2.911 | 4.61 | 0.93 | 1.160 | > | 2.454 | 4.96 | 0.87 | 0.872 | > | 2.425 | 6.89 | 0.87 | 0.825 | > | 2.397 | 4.68 | 0.87 | 0.873 | > | 2.182 | 6.79 | 0.84 | 0.830 | > | 2.142 | 5.54 | 0.84 | 0.856 | > | 1.870 | 5.46 | 0.60 | 1.205 | > | 1.857 | 11.65 | 0.54 | 1.570 | > ------------------------------------------------ > > Possible reasons for the presence of the reported > unexpected low or elevated mean intensity in > a given resolution bin are : > - missing overloaded or weak reflections > - suboptimal data processing > - satelite (ice) crystals > - NCS > - translational pseudo symmetry (detected elsewhere) > - outliers (detected elsewhere) > - ice rings (detected elsewhere) > - other problems > Note that the presence of abnormalities > in a certain region of reciprocal space might > confuse the data validation algorithm throughout > a large region of reciprocal space, even though > the data is acceptable in those areas. > > > Possible outliers > Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 > > Acentric reflections: > > ----------------------------------------------------------------- > | d_space | H K L | |E| | p(wilson) | p(extreme) | > ----------------------------------------------------------------- > | 2.114 | -18, -9, 35 | 3.79 | 5.57e-07 | 5.08e-02 | > | 3.066 | -16, -8, 12 | 3.93 | 1.90e-07 | 1.77e-02 | > | 3.066 | 16, 8, 12 | 3.95 | 1.69e-07 | 1.57e-02 | > | 2.115 | 18, 9, 35 | 3.79 | 5.65e-07 | 5.15e-02 | > ----------------------------------------------------------------- > > p(wilson) : 1-(1-exp[-|E|^2]) > p(extreme) : 1-(1-exp[-|E|^2])^(n_acentrics) > p(wilson) is the probability that an E-value of the specified > value would be observed when it would selected at random from > the given data set. > p(extreme) is the probability that the largest |E| value is > larger or equal then the observed largest |E| value. > > Both measures can be used for outlier detection. p(extreme) > takes into account the size of the dataset. > > > Centric reflections: > > None > > > Ice ring related problems > > The following statistics were obtained from ice-ring > insensitive resolution ranges > mean bin z_score : 3.46 > ( rms deviation : 1.89 ) > mean bin completeness : 0.89 > ( rms deviation : 0.09 ) > > The following table shows the z-scores > and completeness in ice-ring sensitive areas. > Large z-scores and high completeness in these > resolution ranges might be a reason to re-assess > your data processsing if ice rings were present. > > ------------------------------------------------ > | d_spacing | z_score | compl. | Rel. Ice int. | > ------------------------------------------------ > | 3.897 | 0.51 | 0.97 | 1.000 | > | 3.669 | 1.87 | 0.97 | 0.750 | > | 3.441 | 4.52 | 0.96 | 0.530 | > | 2.671 | 3.84 | 0.89 | 0.170 | > | 2.249 | 3.61 | 0.87 | 0.390 | > | 2.072 | 3.23 | 0.82 | 0.300 | > | 1.948 | 0.62 | 0.76 | 0.040 | > | 1.918 | 0.44 | 0.73 | 0.180 | > | 1.883 | 5.46 | 0.60 | 0.030 | > ------------------------------------------------ > > Abnormalities in mean intensity or completeness at > resolution ranges with a relative ice ring intensity > lower then 0.10 will be ignored. > > No ice ring related problems detected. > If ice rings were present, the data does not look > worse at ice ring related d_spacings as compared > to the rest of the data set > > > > > Basic analyses completed > > ##----------------------------------------------------## > ## Twinning Analyses ## > ##----------------------------------------------------## > > > > Using data between 10.00 to 2.87 Angstrom. > > Determining possible twin laws. > > The following twin laws have been found: > > --------------------------------------------------------------------------------- > | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | > --------------------------------------------------------------------------------- > | PM | 2-fold | 0.009 | 0.010 | 0.000 | -h,-k,l | > | PM | 2-fold | 0.090 | 0.079 | 0.001 | -h,-h+k,-l | > | PM | 2-fold | 0.099 | 0.080 | 0.001 | h,h-k,-l | > --------------------------------------------------------------------------------- > M: Merohedral twin law > PM: Pseudomerohedral twin law > > 0 merohedral twin operators found > 3 pseudo-merohedral twin operators found > In total, 3 twin operator were found > > > Number of centrics : 0 > Number of acentrics : 27599 > > Largest patterson peak with length larger then 15 Angstrom > > Frac. coord. : 0.119 -0.276 -0.000 > Distance to origin : 16.337 > Height (origin=100) : 5.893 > p_value(height) : 7.365e-01 > > The reported p_value has the following meaning: > The probability that a peak of the specified height > or larger is found in a Patterson function of a > macro molecule that does not have any translational > pseudo symmetry is equal to 7.365e-01 > p_values smaller then 0.05 might indicate > weak translation pseudo symmetry, or the self vector of > a large anomalous scatterer such as Hg, whereas values > smaller then 1e-3 are a very strong indication for > the presence of translational pseudo symmetry. > > > > Wilson ratio and moments > > Acentric reflections > <I^2>/<I>^2 :1.932 (untwinned: 2.000; perfect twin 1.500) > <F>^2/<F^2> :0.820 (untwinned: 0.785; perfect twin 0.885) > <|E^2 - 1|> :0.678 (untwinned: 0.736; perfect twin 0.541) > > > > NZ test (0<=z<1) to detect twinning and possible translational NCS > > > ----------------------------------------------- > | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | > ----------------------------------------------- > | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | > | 0.1 | 0.046 | 0.095 | 0.000 | 0.248 | > | 0.2 | 0.127 | 0.181 | 0.000 | 0.345 | > | 0.3 | 0.210 | 0.259 | 0.000 | 0.419 | > | 0.4 | 0.287 | 0.330 | 0.000 | 0.474 | > | 0.5 | 0.361 | 0.394 | 0.000 | 0.520 | > | 0.6 | 0.427 | 0.451 | 0.000 | 0.561 | > | 0.7 | 0.486 | 0.503 | 0.000 | 0.597 | > | 0.8 | 0.544 | 0.551 | 0.000 | 0.629 | > | 0.9 | 0.597 | 0.593 | 0.000 | 0.657 | > | 1.0 | 0.643 | 0.632 | 0.000 | 0.683 | > ----------------------------------------------- > | Maximum deviation acentric : 0.055 | > | Maximum deviation centric : 0.683 | > | | > | <NZ(obs)-NZ(twinned)>_acentric : -0.024 | > | <NZ(obs)-NZ(twinned)>_centric : -0.467 | > ----------------------------------------------- > > > L test for acentric data > > using difference vectors (dh,dk,dl) of the form: > (2hp,2kp,2lp) > where hp, kp, and lp are random signed integers such that > 2 <= |dh| + |dk| + |dl| <= 8 > > Mean |L| :0.441 (untwinned: 0.500; perfect twin: 0.375) > Mean L^2 :0.267 (untwinned: 0.333; perfect twin: 0.200) > > The distribution of |L| values indicates a twin fraction of > 0.08. Note that this estimate is not as reliable as obtained > via a Britton plot or H-test if twin laws are available. > > > > --------------------------------------------- > Analysing possible twin law : -h,-k,l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.053 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.005 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.447 > Estimation of twin fraction via cum. dist. of H: 0.449 > > > > Britton analyses > > Extrapolation performed on 0.47 < alpha < 0.495 > Estimated twin fraction: 0.442 > Correlation: 0.9953 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.054 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.004 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.415 > > > --------------------------------------------- > Analysing possible twin law : -h,-h+k,-l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.093 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.015 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.407 > Estimation of twin fraction via cum. dist. of H: 0.407 > > > > Britton analyses > > Extrapolation performed on 0.44 < alpha < 0.495 > Estimated twin fraction: 0.399 > Correlation: 0.9959 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.093 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.011 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.361 > > > --------------------------------------------- > Analysing possible twin law : h,h-k,-l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.085 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.013 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.415 > Estimation of twin fraction via cum. dist. of H: 0.417 > > > > Britton analyses > > Extrapolation performed on 0.46 < alpha < 0.495 > Estimated twin fraction: 0.411 > Correlation: 0.9961 > > R vs R statistic: > R_abs_twin = <|I1-I2|>/<|I1+I2|> > Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95 > > R_abs_twin observed data : 0.086 > > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.009 > No calculated data available. > R_twin for calculated data not determined. > > > Maximum Likelihood twin fraction determination > Zwart, Read, Grosse-Kunstleve & Adams, to be published. > > > The estimated twin fraction is equal to 0.350 > > > > Exploring higher metric symmetry > > The point group of data as dictated by the space group is P 1 > the point group in the niggli setting is P 1 > The point group of the lattice is Hall: C 2 2 (x+y,2*y,z) > A summary of R values for various possible point groups follow. > > ----------------------------------------------------------------------------------------------- > | Point group | mean R_used | max R_used | mean R_unused | min R_unused | choice | > ----------------------------------------------------------------------------------------------- > | Hall: C 2y (x-y,2*x,z) | 0.086 | 0.086 | 0.054 | 0.054 | | > | P 1 | None | None | 0.070 | 0.054 | | > | Hall: C 2y (x+y,2*y,z) | 0.093 | 0.093 | 0.054 | 0.054 | | > | Hall: C 2 2 (x+y,2*y,z) | 0.070 | 0.086 | None | None | | > | P 1 1 2 | 0.054 | 0.054 | 0.093 | 0.093 | <--- | > ----------------------------------------------------------------------------------------------- > > R_used: mean and maximum R value for symmetry operators *used* in this point group > R_unused: mean and minimum R value for symmetry operators *not used* in this point group > The likely point group of the data is: P 1 1 2 > > Possible space groups in this point groups are: > Unit cell: (52.1638, 108.226, 64.5258, 90, 113.762, 90) > Space group: P 1 2 1 (No. 3) > > Unit cell: (52.1638, 108.226, 64.5258, 90, 113.762, 90) > Space group: P 1 21 1 (No. 4) > > Note that this analyses does not take into account the effects of twinning. > If the data is (allmost) perfectly twinned, the symmetry will appear to be > higher than it actually is. > > > > > > ------------------------------------------------------------------------------- > Twinning and intensity statistics summary (acentric data): > > Statistics independent of twin laws > - <I^2>/<I>^2 : 1.932 > - <F>^2/<F^2> : 0.820 > - <|E^2-1|> : 0.678 > - <|L|>, <L^2>: 0.441, 0.267 > Multivariate Z score L-test: 3.807 > The multivariate Z score is a quality measure of the given > spread in intensities. Good to reasonable data is expected > to have a Z score lower than 3.5. > Large values can indicate twinning, but small values do not > neccesarily exclude it. > > > Statistics depending on twin laws > ------------------------------------------------------------------- > | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | > ------------------------------------------------------------------- > | -h,-k,l | PM | 0.054 | 0.442 | 0.449 | 0.415 | > | -h,-h+k,-l | PM | 0.093 | 0.399 | 0.407 | 0.361 | > | h,h-k,-l | PM | 0.086 | 0.411 | 0.417 | 0.350 | > ------------------------------------------------------------------- > > Patterson analyses > - Largest peak height : 5.893 > (correpsonding p value : 7.365e-01) > > > The largest off-origin peak in the Patterson function is 5.89% of the > height of the origin peak. No significant pseudotranslation is detected. > > The results of the L-test indicate that the intensity statistics > are significantly different then is expected from good to reasonable, > untwinned data. > As there are twin laws possible given the crystal symmetry, twinning could > be the reason for the departure of the intensity statistics from normality. > It might be worthwhile carrying refinement with a twin specific target function. > > Note that the symmetry of the intensities suggest that the assumed space group > is too low. As twinning is however suspected, it is not immediuatly clear if this > is the case. Carefull reprocessing and (twin)refinement for all cases might resolve > this question. > > -------------------------------------------------------------------------------

1 0

R, Rfree, and wxu_scale
by Jianghai Zhu 05 Aug '07

05 Aug '07

Hi, Just finished a round of refinement. Rfree went up about 1% and R went down a bit. I am wondering what happened here. Also Rfree always went down after TLS refinement but always went up a lot more after the individual ADP refinement. Is there anything I can do here? Should I use weaker B restraints? I tried to assign a wxu_scale value. But phenix.refine automatically adjust it to 1.81 every time. ------------------------------------------------------------------------ R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3982 0.5701 6.156859e+00 6.238509e+00 1_bss: 0.2008 0.2494 5.949117e+00 6.088855e+00 1_xyz: 0.2030 0.2497 5.953829e+00 6.091696e+00 1_adp: 0.1998 0.2559 5.952833e+00 6.099340e+00 2_bss: 0.1996 0.2557 5.952517e+00 6.099196e+00 2_xyz: 0.1984 0.2576 5.953246e+00 6.104085e+00 2_adp: 0.1974 0.2578 5.950434e+00 6.102336e+00 3_bss: 0.1972 0.2574 5.950333e+00 6.102222e+00 3_xyz: 0.1997 0.2576 5.956524e+00 6.103647e+00 3_adp: 0.1987 0.2590 5.955554e+00 6.104434e+00 3_bss: 0.1986 0.2588 5.955445e+00 6.104227e+00 ------------------------------------------------------------------------ Weights for target T = Exray * wxc * wxc_scale + Echem * wc and angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/d_sites) stage wxc wxu wxc_sc wxu_sc /_gxc,gc /_gxu,gu 0 : 5.5611e-01 7.2249e-01 0.050 1.810 96.334 101.736 1_bss: 5.5611e-01 7.2249e-01 0.050 1.810 96.334 101.736 1_xyz: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 1_adp: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 2_bss: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 2_xyz: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 2_adp: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 3_bss: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 3_xyz: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 3_adp: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 3_bss: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 ------------------------------------------------------------------------ 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 +++++++++++++++++++++++++++++++

3 9

Postdoctoral Position for PHENIX development
by Paul D. Adams 02 Aug '07

02 Aug '07

======================================================================= Lawrence Berkeley National Laboratory Computational Postdoctoral Fellow ======================================================================= Computational Postdoctoral Fellow Job ID: 20907 Division: Physical Biosciences Date Opened: 8/2/2007 Summary We are seeking an intelligent, motivated scientist to develop graphical tools for the PHENIX software system. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities will include development and implementation of graphical interfaces, user workflow tools, and mechanisms for data tracking and storage. Duties Essential - Primary duties and responsibilities will include development and implementation of computational algorithms for structure determination using X-ray crystallography. Develop graphic interfaces to components of the PHENIX software system. Create interfaces between PHENIX and other software packages such as Coot. Implement software code for capturing and tracking data and other information as it is created by the PHENIX software. This position requires interaction with P.I.s, postdocs, Scientists and external collaborators involved in the PHENIX project. Publication of research results in scientific journals and presentation of results at scientific meetings. Marginal - Actively participate in group meetings. Assume shared responsibility for maintenance of computational equipment with other group members. Qualifications Essential - Ph.D. within the last three years in computational crystallography or a related field. Demonstrated experience with graphical interface development. First-author publications in macromolecular crystallography or closely related field. Familiarity with software development tools such as C++, C or Fortran programming languages and scripting languages such as Python or Perl. Strong programming skills. Solid interpersonal skills and the ability to work in a team environment are critical. Marginal - Experience with the practical aspects of protein crystallography: protein production, crystallization and structure solution. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about PHENIX visit: http://www.phenix-online.org/ For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20907. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

1 0

estimated coordinate error
by Jianghai Zhu 01 Aug '07

01 Aug '07

Hi, I am refining a 2.6 A structure using both phenix.refine and refmac5. Both programs give me similar R and Rfree values. But the estimated coordinate errors are quite different. From phenix.refine: maximum likelihood estimate for coordinate error: 0.42 A From refmac5: estimated overall coordinate error: ESU based on R value: 0.427 A ESU based on Free R value: 0.293 A ESU based on maximum likelihood: 0.239 A I am wondering why they are different. 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 +++++++++++++++++++++++++++++++

3 4

General Question !!!
by john kryst 01 Aug '07

01 Aug '07

Hi all !! Please bare with me.. one general very basic question. Do we use electrostatic charges in x-ray refinement. regards John

5 6

AutoSol problem
by Ben Eisenbraun 31 Jul '07

31 Jul '07

Hi- One of my users is running the Linux 64-bit version of Phenix-1.3b and they are getting the following message at the end of their logfile: ************************************************************ Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked ************************************************************ The solve part of Phenix looks like it built correctly: $ ls -l phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/ -rwxr-xr-x 1 sbgrid sbgrid 1561344 Jun 27 16:55 extract_segment -rwxr-xr-x 1 sbgrid sbgrid 1561344 Jun 27 16:55 extract_segment_pair -rwxr-xr-x 1 sbgrid sbgrid 3483160 Jun 27 16:55 resolve -rwxr-xr-x 1 sbgrid sbgrid 3483576 Jun 27 16:55 resolve_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 3483256 Jun 27 16:55 resolve_giant -rwxr-xr-x 1 sbgrid sbgrid 3482968 Jun 27 16:55 resolve_huge -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_giant -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_huge -rwxr-xr-x 1 sbgrid sbgrid 1547840 Jun 27 16:55 segment_library -rwxr-xr-x 1 sbgrid sbgrid 1575648 Jun 27 16:55 side_chains -rwxr-xr-x 1 sbgrid sbgrid 1566208 Jun 27 16:55 side_chains_update -rwxr-xr-x 1 sbgrid sbgrid 5327984 Jun 27 16:55 solve -rwxr-xr-x 1 sbgrid sbgrid 11331152 Jun 27 16:55 solve_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 6529136 Jun 27 16:55 solve_giant -rwxr-xr-x 1 sbgrid sbgrid 7729424 Jun 27 16:55 solve_huge -rwxr-xr-x 1 sbgrid sbgrid 11393392 Jun 27 16:55 solve_mx $ file phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.0, statically linked, for GNU/Linux 2.4.0, stripped We do have a standalone Solve install with its corresponding SOLVEDIR, etc, environment variables. Could that be confusing Phenix? I have the complete logfile, but it's rather long. If it would help, it can be made available. Any ideas on what I should do to troubleshoot this? Thanks. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/

2 2

TEST - please ignore
by Luca Jovine 31 Jul '07

31 Jul '07

Sorry, just re-testing whether my e-mails to phenixbb are still vanishing into nowhere...

1 0

A question about AutoBuild
by Marcelo Carlos Sousa 31 Jul '07

31 Jul '07

We have solved (in part) a structure by Molecular Replacement. The protein is a homodimer with 360 amino acids per chain (one dimmer per asu). The model was pretty good for the last 220 amino acids or so but appears to be wrong for the first 140 so I deleted them and refined using phenix to an R free of ~ 0.38. As I was about to start model building in O I thought I would give the phenix autobuild a try. The resolution is 2.5 Å and the map shows buildable features for the missing domain. I ran the autobuild wizard with RESOLVE building “in- place” to extend the current model. However the program seemed unable to add fragments of secondary structure (even as alanines) to the model. The question is: is the building “in-place” restricted to “growing” the current model from the ends? Marcelo

2 1

part II. A question about autobuild
by Marcelo Carlos Sousa 30 Jul '07

30 Jul '07

I also noticed that water molecules are assigned to the buildable parts of the map.

1 0

R-factor problem !!!
by john kryst 30 Jul '07

30 Jul '07

Hi all !! I am using phenix.refine to refine my 3.2 A structure. Also i use xtal_pdbsubmission utility in CNS to generate pdb file which is submission ready format. Please note no refinement in CNS only formating. Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ?? As for as i know we cant generate a submission ready PDB format from phenix.refine. Is it possible to implement it, which will be very helpful for all of us. Thanks in advance for your inputs regards John

5 7

problems with clashes
by Lari Lehtio 30 Jul '07

30 Jul '07

Hi, I nowadays use phenix.refine almost always in the first stages of the refinement and later usually move to refmac. Now I have two modest resolution structures which behave much better in phenix than in refmac. In addition to the more tedious deposition (I guess), I have a problem with clashes. When I analyse the structures with molprobity, I get much better clashscores with refmac refined files. Is there a way to increase the restraint for these contacts or should I just keep decreasing the wxc_scale (from the default)? Rmsds reported by refmac (0 cycles) for bonds and angles are already lower than what I'm used to. B-factors on the other hand seem to be less restrained in phenix. ~Lari~ _______________________________________ Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________

5 8

Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 27 Jul '07

27 Jul '07

Hi Jianghai, > I tried "discard_psi_phi=False" in phenix.refine. There is only > slightly improvement in the R, Rfree, and ramachandran plot (about > 0.2% less disallowed residues, wxc_scale=0.2). A structure > optimization (wxc_scale=0) with the phi-psi restraints has a bigger > impact (about 2% less disallowed residues) with about 2% higher > Rfree. Thanks for your feedback! > What do you think is a good value for wxc_scale in a low-resolution > refinement? This is a tough one to answer. wxc_scale reflects how much you trust your data to guide you to the best model. That depends on many influences. I think the best - although expensive - approach is to simply try a range of values. Note that the esd on the psi-phi restraints are just someone's (?) best guesses. It may be worth playing with these values as well. For that, copy the data_link_TRANS, data_link_PTRANS, data_link_CIS, and data_link_PCIS blocks from mon_lib_list.cif to a new files, change the values, then specify the file on the phenix.refine command line. (You may want to double-check in the .geo file that your new values are actually used.) > What is the difference between wxc_scale=0 and > phenix.geometry_minimization? Should basically be the same, but in phenix.refine you can override parameters like discard_psi_phi. phenix.geometry_minimization doesn't allow you to do this (it is one of those many little things I never got to). Ralf

1 0

Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 26 Jul '07

26 Jul '07

Hi Jianghai, > I am refining a low resolution huge protein structure. There are > about 20% residues in the disallowed region of ramachandran plot. Is > there a way in phenix.refine to refine the phi, psi angles to get a > better ramachandran plot? or a phi, psi restraints in refinement? If you add discard_psi_phi=False to the phenix.refine command line the psi and phi dihedral angles are restraint according to the CCP4 monomer library definitions in mon_lib_list.cif (run phenix.where_mon_lib_list_cif to get the full path name). Look for data_link_TRANS and data_link_CIS, scroll down to _chem_link_tor.value_angle, to see the restraint definitions. We don't have much experience using the phi, psi restraints. If you don't mind, please let us know how it goes! Ralf

4 5

ramachanran plot refinement or restraint?
by Jianghai Zhu 26 Jul '07

26 Jul '07

Hi, I am refining a low resolution huge protein structure. There are about 20% residues in the disallowed region of ramachandran plot. Is there a way in phenix.refine to refine the phi, psi angles to get a better ramachandran plot? or a phi, psi restraints in refinement? Thanks. 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 +++++++++++++++++++++++++++++++

2 1

problems in installation of phenix
by tara kashav 25 Jul '07

25 Jul '07

Dear all, I am trying to install phenix but getting following error. My system specifications are: 2.6.5-1.358 i686. Can anyone suggest me how to troubleshoot and install the program. Traceback (most recent call last): File "/usr/local/phenix-1.3b/phenix/wxGUI/wxPhenix.py", line 11, in <module> import wx File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libXfixes.so.3: cannot open shared object file: No such file or directory Thanks, Tara Kashav, Dr. S. Gourinath's Lab, Lab No 430, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067

2 1

Re: [phenixbb] How to keep a custom bond planar ?
by Ralf W. Grosse-Kunstleve 24 Jul '07

24 Jul '07

Hi Mathieu, Also sorry for the late reply. > How can I define a plan or some dihedral ?? Sorry, this is not implemented (not hard, but never got to it). > Or as in the ligand .cif I defined a plan > LIG plan-2 C1 0.020 > LIG plan-2 C2 0.020 > LIG plan-2 C3 0.020 > > I could add the atoms NZ and CE of the lysine to the plan-2. You can define the bond, angles, dihedrals, chiralities and planarities with a cif link. Currently we don't generate such links automatically (it is in the works). To get a start, copy one of the links from the mon_lib_list.cif file; the command phenix.where_mon_lib_list_cif will give you the absolute path. Give the cif link a unique name and modify it for your situation. Then use "apply_cif_link" as described in the phenix.refine documentation, e.g. at the CCI Apps download page (http://www.phenix-online.org/download/cci_apps/). Let me know if you need more specific help. Ralf

1 0

Re: [phenixbb] handling of alternate conformations
by Ralf W. Grosse-Kunstleve 24 Jul '07

24 Jul '07

Hi Ulrich, Sorry for the late reply. I was out of town for a week. > My first question is whether NCS constraints are also applied to alternate > conformations. Should be, but is not heavily tested. All NCS restraints are listed in the .geo file created by phenix.refine (assuming write_geo_file=True, which is the default). Look for the long lists following "NCS restraint group". Do your alternative conformation atoms appear in these lists? > My second question concerns the atom count of the conformers, where the > parts with non-alternating conformations seem to be included as well. Pavel's explanation from last week is correct. Internally a "conformer" is always a complete chain. The bond, angle, dihedral, chirality, and planarity restraints are determined independently for each conformer. This generates duplicate restraints which are checked for consistency and then reduced again. Ralf

1 0

handling of alternate conformations
by Ulrich Baumann 16 Jul '07

16 Jul '07

Dear Phenix experts, we encounter the following "problem" when trying to refine alternating conformations: we have a complex with 4 chemically different polypeptide chains in the asymmetric unit, composition A3B3CD. For chains C and D we see additional density, which appears to belong to three alternating conformations which can be thought as rigid-body motions (for the whole chains C and D, let's call these conformers 1,2 and 3, but we label them conventionally in the file with the prefix A,B,and C) with roughly estimated occupancies of about 0.3, 0.3 and 0.4 (we can really see most of them). A and B have no visible alternating conformations (occupancies set to 1.0). From the atom count it appears that phenix reads in three conformers called A,B and C with A: A3B3C(1)D(1), B: A3B3C(2)D(2) and C: A3B3C(3)D(3). Phenix.refine says it has these 3 conformers: conformer A A:2700 atoms, conformer B:2700 atoms, common with A 2100, conformer C:2700 atoms, common with A 2100, common with B 2100. Refinement yields an R/Rfree of about 0.210/0.325. If we treat the three conformers of polypeptide chains C and D as independent chains with occupancy each 1.0 (this is possible 'cos there are no repulsive contacts between them, fortunately), we get R/Rfree of 0.243/0.291 and phenix applies NCS restraints to all chains. The resolution is about 2.9 A. We use phenix.refine from the CCI_APPS, version 2007-03-26-1903, SUSE Linux. My questions is: is the difference due to the lack of NCS between conformers or are the occupancies mistreated somwhow? I am asking because I would not consider the whole A3B3C(x)D(x) particle as a conformer but only chains C and D ...... Is there a possibility to apply NCS restraints to conformers? Many thanks in advance, Ulrich

2 3

How to keep a custom bond planar ?
by Coincon Mathieu 16 Jul '07

16 Jul '07

Hi, I defined a bond (and angles) between my ligand and the NZ of a lysine in a file (bond.def). ..-C2-.. | -CE-NZ = C1-C3-.... This is a double bond. Everything work good except for the planarity of the lysine's atoms. For the bond I wrote in my bond.def: bond { action = *add atom_selection_1 = chain D and resname LIG and name C2 atom_selection_2 = chain A and resname LYS and resid 66 and name NZ distance_ideal = 1.340 sigma = 0.02 } For an angle: angle { action = *add atom_selection_1 = chain D and resname LIG and name C3 atom_selection_2 = chain D and resname LIG and name C2 atom_selection_3 = chain A and resname LYS and resid 66 and name NZ angle_ideal = 120.000 sigma = 3 } How can I define a plan or some dihedral ?? Or as in the ligand .cif I defined a plan LIG plan-2 C1 0.020 LIG plan-2 C2 0.020 LIG plan-2 C3 0.020 I could add the atoms NZ and CE of the lysine to the plan-2. Thanks by advance. And by the way phenix (with coot) is GREAT (I did my apo-enzyme in four days !!!!) -------- Mathieu Coicon PhD Student Biochimie Universite de Montreal (+1)514-343-6111 #5352

1 0

Phaser
by john kryst 13 Jul '07

13 Jul '07

Hi all !!! Is it possible to fix one domain and search for the second one in phaser !!! What are the keywords to use for that. I have a protein with two domains. It i give both the domains together it is not finding the solution. If i give only one domain it is giving the solution and the R and Rfee is 28 and 33. But it is not finding the second one. Thanks in advance for your suggestions.. regards John

2 1