- phenixbb - phenix-online.org

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 03 Sep '07

03 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 22 Aug '07

22 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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