- phenixbb - phenix-online.org

phenix.refine abort
by sujata halder 27 Aug '14

27 Aug '14

Hi, I am trying to refine a protein with 60 chains (a T=1 virus; 5-3-2 symmetry) and each chain has 520 amino acids. I am using version 1.9 (Release tag: 1692). The job stopped midway and gave the error below followed by "Cannot allocate memory". I have run a similar job (i.e using a similar sized protein) before on an older version (version 1.7) and that had worked. Looking at the error I can't really figure out if the problem is related to installation or a missing module or something different about the code. I can share my files off-list. Here is the error: ====================== XYZ individual (reciprocal space) ====================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 28.80 29.29 0.49 0.016 1.6 11.9 0.8 7.4 60 none 0.093 160.8996 Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/command_line.py", line 163, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/driver.py", line 1577, in run reference_model_manager = self.reference_model_manager).result File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/strategies.py", line 183, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 114, in __init__ self.call(self.xyzrec, "XYZ individual (reciprocal space)") File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 142, in call func(prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 374, in xyzrec prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 204, in __init__ call_back=(len(trial_weights)==1)) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 314, in try_weight result = self.show(weight=wt, print_stats=print_stats, call_back=call_back) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 365, in show molprobity_scores = self.main.use_molprobity) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model.py", line 1341, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model_statistics.py", line 99, in __init__ self.clashscore = clashscore(pdb_hierarchy=pdb_hierarchy).get_clashscore() File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 133, in __init__ verbose=verbose) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 257, in __init__ self.run_probe_clashscore(self.h_pdb_string) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 341, in run_probe_clashscore stdin_lines=pdb_string).raise_if_errors().stdout_lines File "/usr/local/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 158, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 709, in __init__ errread, errwrite) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 1222, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory ------------------------------------------------------------------------------------------------------------- Thanks, Sujata

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Missing sanity check of duplicate resids within one chain?
by Schubert, Carsten [JRDUS] 27 Aug '14

27 Aug '14

Hi, this is a bit of an esoteric issue I just stumbled over, but I'd like to flag this up anyhow. For some reason (most likely boneheaded error on my side) I wound up with duplicate resids for two ion-atoms: TER HETATM 9325 CL CL S 1 10.578 23.153 35.662 1.00 75.71 Cl1- HETATM 9326 CL CL S 2 -6.546 32.210 31.507 1.00 80.31 Cl1- HETATM 9327 CL CL S 3 21.899 28.037 25.883 1.00 86.22 Cl1- HETATM 9328 K K S 3 7.259 -0.149 19.530 1.00 91.09 K1+ TER Phenix (1.9-1692) seemingly happily accepted the input and proceeded with refinement and validation. After upgrading my coot installation to the latest build the error was flagged. I think this sort of mistake should have at least been flagged in the validation stage or is this out of scope for phenix? Cheers, Carsten

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phenix.maps command line arguments
by Ryan McGreevy 26 Aug '14

26 Aug '14

When using phenix.maps from the command line, passing any arguments for the "map" layer of parameters does not seem to work. For example the command: phenix.maps input.pdb_file_name=input.pdb input.reflection_data.file_name=input.mtz works just fine, but parameters under the "map" section don't seem to have any effect, such as: map.file_name=map.ccp4 map.kicked=True Could I be doing something wrong, or does this not actually work? I know I can set these parameters in a maps.params file, but I would like to be able to pass them on the command line for scripting and automation purposes.

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following on the anomalous map
by CPMAS Chen 26 Aug '14

26 Aug '14

Hi, All Phenix users, I am following this topic. http://www.phenix-online.org/pipermail/phenixbb/2014-April/020622.html. Here is the point I am not clear. If I am using phenix.refine to generate LLG map, how do I pick the anomalous group since I have not placed them in the model yet? By the way, when I choose ion_placement and specify Br, the result comes with no Br. Let me make my situation clear first. I want to find whether the Br-containing ligand is seen in my protein which I have a high resolution structure available. I have data collected at Br wavelength, peak or higher position. Phenix.xtriage reported that the anomalous signal is present to about 4A. However, both AutoSol or MR-SAD cannot identify the Br position. Simply say, AutoSol or MR-SAD can not generate any solution. Well, of course, the simple answer would be that there is no such ligand cocrystallized. Anyway, I am trying to see if the anomalous difference map or LLG(generated by phenix.maps, this would be the initial one I assume) can tell me anything more useful. So, my question on this topic would be what is a better way you guys would recommend to identify these Br-ligands? By the way, I did have the native datasets for the same protein with ligand. Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Header accuracy after only refining ligands
by Katherine Sippel 26 Aug '14

26 Aug '14

Hi all, I was trying to prep a structure for PDB deposition. All the protein atoms were good, but I needed to correct some ADP and ligand issues. I ran coordinate refinement only on the ligands and subsequent ADP refinement. Everything was good, except the RSMD values output are clearly only for the ligands. Now I am wondering which values in the header I can trust as far as deposition goes. I tried to do a workaround where I ran refine with 0 macrocycles to see if I could get the proper values, but obviously the bulk solvent is different and I get higher R values. I am wondering if I can run validation to get the correct RMSD values or if there are other header values that might have been affected by not refining all the coordinates? Cheers, Katherine -- "Nil illegitimo carborundum"* - *Didactylos

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DEN refinement
by marinabb phenix 25 Aug '14

25 Aug '14

Dear all, I am trying to use DEN refinement as implemented in the Phenix-1.9 release to refine a structure at 3.6 Angstrom resolution. The asu consists of 8 copies of hetero-dimers (of roughly 40 KDa sunbunits each). The structure of one of the subunits has already been solved at about 2 Angstrom, whereas for the other no homologous model is available. After automatic + manual building, I have now a model with Rfree = 28 / R = 23, with some protomers better built than others. I have used this pdb model as input for DEN refinement, adding the known higher-resolution structure as a (partial) reference model, and ncs restraints previously found (and run a DEN parameters optimisation). The final DEN Rfee got significantly worse. I would appreciate any advise for a better DEN strategy to be adopted in this case, if possible. In particular I was wondering whether it can be worth building a model for the missing subunit (or part of it) based on structural similarity of the current unrefined 3D structure. I thank you in advance for the suggestions. With kind regards, Marina ----- Marina Mapelli, PhD Department of Experimental Oncology European Institute of Oncology Via Adamello 16, 20139 Milan, Italy tel: +39-02-94375018 email: marina.mapelli(a)ieo.eu web: http://www.ifom-ieo-campus.it/research/mapelli.php -----

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overlapping electron density maps
by 李翔 25 Aug '14

25 Aug '14

Hi everyone, I am working on a series of crystals with overall same framework structure plus a different extra part which attaches to the framework. I want to compare the electron density maps of the crystals by overlapping the frameworks and see how the extra parts differ from each other. Is there a way I can do it? Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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table_one
by Andreas Förster 24 Aug '14

24 Aug '14

Dear all, I encounter the following error when running phenix.table_one from the command line (RHEL 6.3 64-bit, phenix-dev-1769): andreas@csbstereo in blah: phenix.table_one Traceback (most recent call last): File "/csb/soft/Linux64/share/phenix-dev-1769/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/table_one.py", line 6, in <module> phenix.automation.table_one.run(sys.argv[1:], auto_extract_labels=True, AttributeError: 'module' object has no attribute 'run' Aunt Google insists that this is "a circular import issue". What do the developers say? Thanks. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

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Low resolution refinement
by Appu kumar 24 Aug '14

24 Aug '14

Hello All, I have a data from a crystal which we can process to 4.5A, and we are able to get a good molecular replacement model and it is a tetramer in ASU. I tried refining structure with phenix.refine but Rfree stuck at 0.41. I read a paper published by David Baker and phenix developer in 2013 about the low resolution refinement using a combination of rosseta and phenix. I would appreciate if i get a help on the refinement in rosseta along with phenix. This paper convince me that its worth trying the rosseta and phenix together for low resolution structure refinement. Thank you Appu

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Re: [phenixbb] Phenix Webserver Down?
by Chen Zhao 22 Aug '14

22 Aug '14

Thank you all for the info. It is been like this for me for a week, and it might just be some local issues. On Fri, Aug 22, 2014 at 4:20 PM, Paul Adams <pdadams(a)lbl.gov> wrote: > > Appears to be okay from the Bay Area. > > On Aug 22, 2014, at 1:00 PM, Chen Zhao <c.zhao(a)YALE.EDU> wrote: > > > Dear all, > > > > I am sorry to bother you, but I have problems connecting to > www.phenix-online.org. Does anybody have similar problem? > > > > Thank you, > > Chen > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > -- > Paul Adams > Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley > Lab > Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley > Lab > Adjunct Professor, Department of Bioengineering, U.C. Berkeley > Vice President for Technology, the Joint BioEnergy Institute > Laboratory Research Manager, ENIGMA Science Focus Area > > Building 64, Room 248 > Building 80, Room 247 > Building 978, Room 4126 > Tel: 1-510-486-4225, Fax: 1-510-486-5909 > http://cci.lbl.gov/paul > > Lawrence Berkeley Laboratory > 1 Cyclotron Road > BLDG 64R0121 > Berkeley, CA 94720, USA. > > Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 > ] > -- > > > > > > > > > > > > >

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