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Using phenix.pdbtools to strip multiple conformations out of a PDB file?
by Stephen Graham 04 Aug '09

04 Aug '09

Dear all, Apologies if this is a dumb question, but I couldn't find the answer in the docs or by asking the googlebrain. Is there a simple way in phenix.pdbtools to strip "alternate conformations" of side chains, etc, from an input PDB file? By removing "alternate conformations" I mean I would like to keep the conformation with the highest occupancy (not necessarily denoted 'A' in the altLoc column) unless all conformations have an equal occupancy, in which case I'd arbitrarily keep conformation 'A'. I think it should be possible by a clever atom_selection command, but the correct syntax has thus-far eluded me! Thanks, Stephen -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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Is the twin refine conflict with order_solvent refine
by shi jiahai 04 Aug '09

04 Aug '09

Hi, Dear all, I am refine a twin dataset with phenix 1.4-3 and CCI (2008_02_08_1610) on a CenOS 5.2 workstation. When I run refine with twin law or order_solvent alone, the refinement is good. Everything goes smoothly. However if I enable refinement on both twin law and order_solvent, the error comes during the order_solvent refinement as below. Start model: number = 55 b_iso_min = 5.52 (limit = 1.00) b_iso_max = 60.32 (limit = 60.00) b_iso_mean = 24.19 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.13 (limit = 1.80) dist_sol_mol_max = 4.38 (limit = 6.00) Traceback (most recent call last): File "/Application/CCI/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 80, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1162, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 350, in refinement_machine log = log) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 132, in __init__ map_cutoff = self.params.primary_map_cutoff).peaks_mapped() File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 324, in find_peaks log = self.log) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/find_peaks.py", line 65, in __init__ symmetry_flags = maptbx.use_space_group_symmetry) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2238, in electron_density_map w2 = w2).fft_map( File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2126, in map_coefficients "m_gradient" AssertionError Can anybody help me with this? Thanks a lot in advance! Best Regards, Shi Jiahai Department of Biological Sciences, National University of Singapore

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Assertion error while adding water
by Bishal Kumar Singh 03 Aug '09

03 Aug '09

Hi, Following error is showing while adding water. Every command-line is as default except "ordered_solvent = True". I will appreciate your suggestions. "0.7 1.17367178905 0.7 1.2044634853 0.7 1.18455476555 0.7 1.21102571346 0.7 1.20890773595 0.7 1.23028004675 0.7 1.2017635385 0.7 1.2151128962 0.7 1.20672093638 0.7 1.17881942233 0.7 1.21258440895 0.7 1.21100112067 0.7 1.22101928156 0.7 1.20955876073 0.7 1.17722437184 0.7 1.19891104532 0.7 1.18433797592 Traceback (most recent call last): File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.py", line 16, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1121, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 394, in refinement_machine log = log) File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/solvent/ordered_solvent.py", line 159, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/solvent/ordered_solvent.py", line 334, in find_peaks log = self.log) File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/find_peaks.py", line 93, in __init__ crystal_gridding_tags = fft_map.tags() File "/wrkhuge/cci_apps/cci_apps_sources/cctbx/maptbx/__init__.py", line 152, in tags return crystal_gridding_tags(self) File "/wrkhuge/cci_apps/cci_apps_sources/cctbx/maptbx/__init__.py", line 158, in __init__ assert gridding.symmetry_flags() is not None" regards, Bishal Singh

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Autosol error
by Francis E Reyes 01 Aug '09

01 Aug '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 28 Jul '09

28 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 25 Jul '09

25 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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