- phenixbb - phenix-online.org

Run time error while refining
by Subhani Bandara 22 Jun '12

22 Jun '12

Hi everyone, I got the following error message while running refinement in mac, using PHENIX-1.8-1069. This occured when refined after editing Ramachandran outliers in coot, without applying Ramachandran restraints. Not sure wether it has something to do with this. RuntimeError : Estimated memory allocation for cubicles exceeds max_number_of_bytes: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(3528.41,3528.41,3442.53) n_cubicles=(706,706,689) max_number_of_bytes=2147483648 Any suggestions! Thanks Subhani

2 2

error TLS groups
by Christian Roth 22 Jun '12

22 Jun '12

Dear Phenix developers, If I want use the automatic TLS definition the following error appears. At least the first error line with invalid iteral does also appear int the last verification step of the validation against the supplied sequence file. I have a PMS modified Serine could that cause the problem, because with other pdb's it works. Best Regards Christian RuntimeError : Error in subprocess! Original error: invalid literal for int() with base 10: '' Original traceback: File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/libtbx/thread_utils.py", line 233, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", line 901, in __call__ xray_structure=self.xray_structure) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", line 729, in find_tls ssm.find_automatically(log=out) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", line 334, in find_automatically self.sec_str_from_pdb_file = self.find_sec_str(log=log) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", line 381, in find_sec_str allow_none=True) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 425, in process_records secondary_structure = annotation(records=records) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 62, in __init__ self.helices = parse_helix_records(records) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 217, in parse_helix_records helix_class=string.atoi(line[38:40]), File "/userdata-2/christian/phenix-1.8-1069/build/intel- linux-2.6/base/lib/python2.7/string.py", line 403, in atoi return _int(s, base) Traceback (most recent call last): File "/userdata-2/christian/phenix-1.8-1069/phenix/wxGUI2/Programs/Refine/TLS.py", line 140, in OnFindTLS self.find_tls_groups() File "/userdata-2/christian/phenix-1.8-1069/phenix/wxGUI2/Programs/Refine/TLS.py", line 103, in find_tls_groups callback=None) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/wxtbx/process_control.py", line 348, in run_function_as_process_in_dialog dlg.handle_error() File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/wxtbx/process_control.py", line 302, in handle_error %s""" % (str(exception), traceback)) RuntimeError: Error in subprocess! Original error: invalid literal for int() with base 10: '' Original traceback: File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/libtbx/thread_utils.py", line 233, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", line 901, in __call__ xray_structure=self.xray_structure) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", line 729, in find_tls ssm.find_automatically(log=out) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", line 334, in find_automatically self.sec_str_from_pdb_file = self.find_sec_str(log=log) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", line 381, in find_sec_str allow_none=True) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 425, in process_records secondary_structure = annotation(records=records) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 62, in __init__ self.helices = parse_helix_records(records) File "/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", line 217, in parse_helix_records helix_class=string.atoi(line[38:40]), File "/userdata-2/christian/phenix-1.8-1069/build/intel- linux-2.6/base/lib/python2.7/string.py", line 403, in atoi return _int(s, base) -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

2 1

phenix.mr_model_preparation
by Alexander Batyuk 21 Jun '12

21 Jun '12

Dear all, I'm trying to run phenix.mr_model_preparation in phenix 1.8-1069 with a .hhr file but it fails with Reading homology search file: 4671015.hhr Sorry: Uninterpretable: 'Q ss_pred cccccchHHHHHHHHHHHHHHHHHhhhchheEEE etc. Could somebody point me to the right direction, please? Thank you and best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

2 1

phenix.refine and torsion-angle ncs
by Antony Oliver 21 Jun '12

21 Jun '12

Dear phenix.bb How do I specifically exclude particular amino acids from torsion-angle ncs? >From the GUI, it is not obvious. In a couple of my chains, one or two amino acids are in definite crystal contacts, and are therefore in a different rotamer/conformation compared to the other ncs-related copies. Unfortunately, I can't seem to find the right option / keyword to stop the refinement job moving these side-chains to agree with the rotamers found in the other molecules of the asymmetric unit. Many thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

3 4

Re: [phenixbb] bad geometry problem
by Qian Sarah 20 Jun '12

20 Jun '12

> > > Hi Pavel Thank you so much! The information is VERY detailed and I learnt a lot! Thanks to phenixbb! > > 2012/6/21 Pavel Afonine <pafonine(a)lbl.gov> > >> Hi Sarah, >> >> thanks for sending me the data. I spent 15 minutes trying a few things >> and here is the statistics I get: >> >> r_work = 0.2454 r_free = 0.2700 >> MOLPROBITY STATISTICS. >> ALL-ATOM CLASHSCORE : 13.60 >> RAMACHANDRAN PLOT: >> OUTLIERS : 0.89 % >> ALLOWED : 5.33 % >> FAVORED : 93.78 % >> ROTAMER OUTLIERS : 8.64 % >> CBETA DEVIATIONS : 0 >> >> which isn't that bad compared to the starting point: >> >> r_work = 0.2469 r_free = 0.2613 >> MOLPROBITY STATISTICS. >> ALL-ATOM CLASHSCORE : 48.87 >> RAMACHANDRAN PLOT: >> OUTLIERS : 2.49 % >> ALLOWED : 5.33 % >> FAVORED : 92.18 % >> ROTAMER OUTLIERS : 29.47 % >> CBETA DEVIATIONS : 10 >> >> Here is what I did (it's just one of possible ways of doing this; other >> scenarios may works as good as this one or better!): >> >> - add H atoms: >> >> phenix.reduce model.pdb > model_H.pdb >> >> - then run a quick geometry regularization: >> >> phenix.pdbtools model_H.pdb --geom >> >> - then strip off H: >> >> phenix.reduce -trim model_H_regularized.pdb > start.pdb >> >> - then run refinement using NCS and Ramachandran plot restraints: >> >> phenix.refine start.pdb def_data.mtz main.ncs=true --overwrite >> output.prefix=def2 main.number_of_mac=5 ramachandran_restraints=true >> rama_potential=emsley strategy=individual_sites+**individual_adp >> >> - then take outcome of previous refinement and run the same refinement >> plus weights optimization: >> >> phenix.refine def2_001.pdb def_data.mtz main.ncs=true --overwrite >> output.prefix=def3 main.number_of_mac=5 ramachandran_restraints=true >> rama_potential=emsley strategy=individual_sites+**individual_adp >> optimize_xyz=true nproc=6 >> >> Also, looking at the original maps I see a lot of places where simple >> fixing in Coot is just obvious, for both - rotamers and Ramachandran >> outliers. So you should do it first of all. >> >> Also, use Ramachandran restraints ONLY to preserve good starting model >> and NOT to fix problems. >> >> All in all, geometry problems you were concerned about are all easily >> fixable. One of the reason why these problems arise is that the map is >> really looking like 3A resolution map, may be even worse; plus there are >> places in the model that you need to fix manually (refinement would not be >> able to fix them). >> >> I will send you the files off-list. >> >> >> Pavel >> >> On 6/19/12 1:17 AM, Qian Sarah wrote: >> >>> Hi, this may not be a new problem, but I tried every stretagy that I >>> know from bb, but the geometry is still very bad. So I wish I can get some >>> help from here. >>> Crystal information: >>> SAD data. Resolution 3.0. There is no anisotropy in the data. >>> R/Rfree : 22.7/26.8 (Rfree-flag is always from the Refine_data.mtz file >>> generated after the first refinement.) >>> RMS(bonds):0.02 >>> RMS(angles): 1.453 >>> Ramachandran outliers: 3.0% >>> Ramachandran favored: 91.2% >>> Rotamer outliers: 18.7% !! >>> Clashscore: 31.84 >>> overall score: 3.47 >>> I tried different strategies, like autobuild and then refine; set >>> wxu/wxc=0.3/0.3; turn on "Ramachandran restrains", "fix bad sidechain >>> romaters"etc, however the paramters are still very bad, especially the >>> rotamer outliers. Then I rebuild them manually in coot,after refinement the >>> parameters are even worse. >>> p.s. phenix version: phenix-1.7.3-dev-1046. >>> Thank you very much! >>> best, >>> Sarah >>> >> >> >

1 0

fixing weights
by Morten Groftehauge 20 Jun '12

20 Jun '12

Hi all, I tried specifying wxc, wxu, wxu_scale and wxc_scale as you can see from the log file: target_weights { wxc_scale = 0.50001 wxu_scale = 0.49999 fix_wxc = 6 fix_wxu = 0.35 } but the refinement proceeds with the default values for _scale: ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.000000 wxc_scale = 1.000 wc = 1.000 | | angle between x-ray and geometry gradient vectors: None (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.350000 wxu_scale = 0.500 wu = 1.000 | | angle between Xray and ADP gradient vectors: None (deg) | |-----------------------------------------------------------------------------| I am running dev-1082, used the GUI for phenix.refine. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

3 3

R-factor calculation
by Abhinav Kumar 20 Jun '12

20 Jun '12

Hi, Is it possible to specify a different high resolution cutoff (than what's in data file) in phenix.model_vs_data for R-factors calculation? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992

2 4

bad geometry problem
by Qian Sarah 20 Jun '12

20 Jun '12

Hi, this may not be a new problem, but I tried every stretagy that I know from bb, but the geometry is still very bad. So I wish I can get some help from here. Crystal information: SAD data. Resolution 3.0. There is no anisotropy in the data. R/Rfree : 22.7/26.8 (Rfree-flag is always from the Refine_data.mtz file generated after the first refinement.) RMS(bonds):0.02 RMS(angles): 1.453 Ramachandran outliers: 3.0% Ramachandran favored: 91.2% Rotamer outliers: 18.7% !! Clashscore: 31.84 overall score: 3.47 I tried different strategies, like autobuild and then refine; set wxu/wxc=0.3/0.3; turn on "Ramachandran restrains", "fix bad sidechain romaters"etc, however the paramters are still very bad, especially the rotamer outliers. Then I rebuild them manually in coot,after refinement the parameters are even worse. p.s. phenix version: phenix-1.7.3-dev-1046. Thank you very much! best, Sarah

3 3

Source code build - overriding compiler choice
by Graeme Winter 18 Jun '12

18 Jun '12

Hi Folks, On my macbook with lion and a source code build, I always set --compiler=gcc for cctbx and this works fine. Just tried a source code build of phenix which failed because it picked up clang, so how do I override this in the install script? I didn't see the option from the install script: Graemes-MacBook-Pro:phenix-installer-dev-1078 graeme$ ./install --help Usage: install [options] Options: --prefix=<path> Determines PHENIX installation path, which will be <path > /phenix-[version] --overwrite Forces overwriting of installed packages --nproc=number Number of processors to use in compilation --base-only Do not compile PHENIX sources (cctbx, phaser, resolve, etc.) --no-gui Do not compile and install GUI components --no-apps Don't create Mac app launcher icons --app-prefix=<path> Path for Mac app launchers (default: /Applications) --noopt Turn off optimization during compilation --debug Turn on debugging during compilation --openmp Try to use OpenMP if supported by compiler --force-compile Force compilation of source --binary Force a binary install if binaries and source are both available --source Force a source install if binaries and source are both available --no-packages Do not install other packages such as PHASER --alias-mtype=<string> Force installation from a different machine type e.g. --alias-mtype=intel-linux-2.4 [for binary installations only] --try-unsupported Try source installation on an unsupported platform --help Print this help message Thanks, Graeme

2 3

MR_Rosetta
by Heather Condurso 15 Jun '12

15 Jun '12

Hello all, I am working on a structure for which a good molecular replacement model doesn't really exist ( highest sequence similarity is 24% for a protein with completely different function and even worse for proteins with a more similar function). As I try and solve the phase with Se-Met derived protein, I thought I would try and use MR_rosetta and see what happens. I have also tried to use pyrosetta to generate better models, but the structure alignments suggest my protein to be primarily composed of beta sheets so the models from ab initio methods aren't great. I am using the GUI and have given my sca file, a sequence file, the 3 and 9 fragment files, and both the global and local alignment hhr files. I thought that phenix would use the hhr alignments to pull models directly from the pdb, but without giving a model pdb, MR_rosetta fails. So my question is how do I input the models? Should I download each of the pdbs and clean them up a bit? How many should I include? I unde! rstand the more I include the more computing time this will take. Can you give any recommendations as to other parameters to change keep the computing time down initially to identify the best model before extensive time is used? I appreciate any help you may be able to provide, Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

3 6