July 2009 - phenixbb - phenix-online.org

Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 23 Jul '10

23 Jul '10

Hi Scott, Your first command looks good to me. It is saying that the composition of the crystal is 2 copies of each chain: component_1.component_copies=2 component_2.component_copies=2 and you want to search for 2 copies of each of your search models: ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2 All the best, Tom T > Hi Phenixers, > > I'm a bit confused about the proper syntax for my phenix.automr job. > This is probably a simple concept, but I'm running on 3 hours of sleep > as my kid was up all night, and my synapses aren't working so good. > > I expect 2 copies of my protein per AU > > My protein is composed of two domains > > I have a single PDB search model for each domain > > is either of these commands correct? > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=2 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=2 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > or > > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=1 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=1 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > essentially I'm not really using an ensemble of search models, I only > have a single PDB for each domain. So should ensemble_1.copies_to_find > and ensemble_2.copies_to_find be set to 1 or 2? > > > Thanks, > Scott > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.als.lbl.gov > Advanced Light Source > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd > MS6R2100 > Berkeley, CA 94720 > C) 510.206.4418 > O) 510.495.2697 > Beamline) 510.495.2134 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] sigma cutoff
by Kay Diederichs 30 Nov '09

30 Nov '09

> > > Hi, > > According to the Phenix manual, phenix.refine uses no sigma cutoff by > default. Since I haven't changed this manually, why do I see in my pdb > file MIN(FOBS/SIGMA_FOBS) 1.340? > > Thanks for help, > Karolina > > This one I can answer because I asked myself the same question recently. The answer is that Phenix does not impose any sigma cutoff, but rather your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . You can verify this for yourself by going through your reflection file, line by line, and calculating Fobs/Sigma_Fobs for each reflection. You will find that all your reflections have a Fobs/Sigma_Fobs larger or equal to 1.34 . So it has nothing to with phenix; phenix just reports a property of your data. An easier way than doing it "manually" is using CCP4 sftools for calculating a new column "ratio", writing out the resulting MTZ file, and looking at this with mtzdmp. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

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Autosol error
by Francis E Reyes 31 Jul '09

31 Jul '09

All When issuing phenix.autosol native.data=scala_072809B_3_001.mtz deriv.data=scala_072909A_3_001.mtz deriv.atom_type=Ir deriv.sites=5 deriv.inano=noinano native.labels='IMEAN SIGIMEAN' deriv.labels='IMEAN SIGIMEAN' I get the error **************************************** AutoSol Input failed For SIR datasets please enter two datafiles or datasets.(native +deriv) Please treat MIR as a series of SIR datasets ...to specify a particular set of data you can specify one of the following (command-line format shown, for a script take out the '=' and use the keyword 'group_labels_list' instead): native.labels='IMEAN SIGIMEAN' deriv.labels='IMEAN SIGIMEAN' native.labels='I(+) SIGI(+) I(-) SIGI(-)' deriv.labels='I(+) SIGI(+) I(-) SIGI(-)' **************************************** Any ideas? thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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combining models from multi-start simulated annealing
by James Whittle 30 Jul '09

30 Jul '09

Is there a way to use AutoBuild to combine a set of models created by multi-start simulated annealing? I've used a random number generator to seed different SA runs at two temperatures, as suggested on this bulletin board before ... but can combine the best parts of these models automatically? --James

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Integrating Phenix with Torque
by Jeremy Mann 29 Jul '09

29 Jul '09

A new user of mine wants to run Phenix on two of our clusters. We use Torque/Maui as our batch scheduler and would like to integrated their usage of Phenix. They want to run something like: phenix.autobuild data=data.hkl seq_file=seq.dat model=model.pdb multiple_models=True multiple_models_number=20 n_cycle_rebuild_max=5 nbatch=20 nproc=20 The documentation mentions briefly the ability to use batch schedulers but doesn't give examples of submission scripts. -- Jeremy Mann jeremy(a)biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672

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Phaser RMS - What happens when it is too high
by Peter Grey 29 Jul '09

29 Jul '09

Hi all, In Phaser RMS is a crucial parameter. I had several cases where underestimation of RMS resulted in negative LLG. The cure was simply increasing the RMS. But I wonder, are there negative effects to a too high RMS. What are the dangers of giving Phaser a too high RMS ? Are there any indications in the output for that. This is also important with EM maps as models since in that case estimation of RMS is difficult. Many thanks in advance for your advice and insight, Peter.

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phenix.refine issue
by Dennis Wolan 27 Jul '09

27 Jul '09

I am having an issue with running a simple phenix.refine that I have never encountered before. I get a list of issues and the program quits with: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/ refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0): RuntimeError: min() argument is an empty array I have no idea if the issue is with my pdb or mtz. I'm sure it's something very simple that I just am not identifying. Thanks in advance, Dennis

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phaser MR
by sbiswas2＠ncsu.edu 27 Jul '09

27 Jul '09

Hi all, I was trying to solve a structure by molecular replacement. I scaled the data in P4222 space group (resolution 2.7A) with two molecules in the assymmetric unit (molecule A and B) I ran phaser with my model and got a Zscore of 5.1. When I look at the map that I got from phaser I could easily see good electron density for both molecules, However upon inspection of the electron density map there were considerable interaction or clashes with molecule B and a symmetry atom. Molecule A had no clashes however with the symmetry atoms. I was wondering if anyone knows how to resolve this. Could it be a problem of space group. The statistics are good for space group P4222 and the I/sigI was good till 2.7A. Any advice is appreciated, Shya

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question about SAD+MR
by crystallogrphy 24 Jul '09

24 Jul '09

Dear all, I have a Se-Met SAD data which diffracted to 2.8A (peak wavelength). The space group is P1. The map from SAD autosol and autobuild still gives crappy map, I can only see one continous alpha-helix density with all other density fragmented and difficult to identify. I suppose it is because of high mosaicity (1.5), low data redundency, and some radiation damage. Now I want to use mocular replace (sequence identify ~0.26) plus SAD data to give better map. 1. The result from MR is shown below and the density is poor as the sole SAD map: REMARK Log-Likelihood Gain: 121.374 REMARK RFZ=3.4 TFZ=100.0 PAK=0 LLG=29 RFZ=3.7 TFZ=5.4 PAK=0 LLG=69 RFZ=6.1 TFZ=4.0 PAK=0 LLG=97 RFZ=5.6 TFZ=5.0 PAK=0 LLG=118 LLG=121 2. I then tried to combine MR model and SAD data set phenix.autosol seq_file=zntb-sd.seq sites=14 atom_type=Se data=output-peak.sca sg="P1" cell="44.355 56.687 58.451 61.061 82.013 82.740" resolution=3.0 input_partpdb_file=AutoMR_run_1_/MR.1.pdb The program failed to run with such error message: Failed to carry out AutoSol_score_ha_solutions: [Errno 2] No such file or directory: 'AutoSol_run_3_/TEMP0/phaser_mtz.hand.mtz' I do not know where to get this phaser.mtz.hand.mtz file or how to generate it. Does anyone know? -- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: qunwan1(a)gmail.com lab phone: 216-368-3337

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new gui on osx (10.5)
by Miguel Ortiz Lombardia 24 Jul '09

24 Jul '09

Dear all, We would like to run the new phenix GUIs from a remote computer. Both server and clients are OSX 10.5 (leopard) and they have the same versions of software (X11, python, phenix... all them pretty new versions) When trying to do so, we invariably get this error: This program needs access to the screen. Please run with 'pythonw', not 'python', and only when you are logged in on the main display of your Mac. I have searched the internet for similar problems and I found an old (one year) unresolved question on the same/similar issue: http://www.phenix-online.org/pipermail/phenixbb/2008-July/001129.html In our case, the /usr/local directory is not mounted over the NFS, it is local. As in that case, though, changing the LIBTBX_PYEXE_BASENAME to pythonw (for example in the phenix.autosol_gui wrapper) did not solve the issue. However, it is not clear to me that this variable has to be changed in a single place: it is found in many files. My question is: was this issue solved and I missed that? If not, anyone has a clue on how to solve the problem? Just to make it clear, the GUIs work perfectly locally in the server computer, that is, if not exported. Thanks a lot! Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

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