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elbow.builder to generate charges on individual atoms?
by Francis E Reyes 13 Sep '07

13 Sep '07

Ok, this is probably an unsupported feature(TM),but is there anyway to hack elbow.builder to output an electronic charge (presumably from the AM1 calculation) for each atom of a ligand? (by say substituting in for the Bfactor)) 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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Position for PSI Knowledgebase development
by Paul Adams 12 Sep '07

12 Sep '07

======================================================================= Lawrence Berkeley National Laboratory Software Developer II ======================================================================= Software Developer II Job ID: 20930 Division: Physical Biosciences Date Opened: 8/7/2007 Summary This position will be part of the Computational Crystallography Initiative at Lawrence Berkeley Lab and will be responsible for developing a web site to disseminate information about the Technologies developed by the NIH Protein Structure Initiative (PSI). This program funds the majority of structural genomics efforts within the US and is responsible for the development of many new technologies that are useful to macromolecular crystallographers. This technology resource is part of the larger PSI Knowledge Base that will provide an information portal for the scientific community. Duties Essential: Under general direction of the Principal Investigator: Develop and maintain web site documenting PSI developed technologies. Interact with PSI researchers to collect information about new technologies. Create a relational database to store crystallographic data. Install and maintain SVN repositories for the PSI community. Marginal: Perform routine analysis of crystallographic data. Maintain web site computing hardware and software. Other duties as assigned. Qualifications Essential: Experience with writing and maintaining HTML web pages. Knowledge of standard programming methods, and Python in a UNIX environment. Strong analytical and organizational skills. Ability to handle multiple tasks in parallel. Excellent interpersonal skills for working in a diverse team environment, ability to interact effectively with other scientists, and to address their needs in an effective and timely manner. Marginal: B.S. Degree or higher in biophysics, computer science, chemistry, electrical engineering, physics or related field preferred or equivalent experience, with demonstrated programming experience. Experience maintaining computing hardware and software. Experience with analysis of crystallographic data. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20930. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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pseudo-merohedral twinning in P212121
by Schneider Sabine 12 Sep '07

12 Sep '07

Hi everyone, I have a data set to 2.8A, with most likely 2 molecules in the asu and a molecular replacement model with 40% sequence identity. (Cell 71.3 71.3 227.9 90 90 90) Initially the data appeared to be either P4322 or P43212 (Rsym = 7.4%; Cell 71.3 71.3 227.9 90 90 90), but the molecular replacement solutions had major clashes with the symmetry related molecules and a lower LLG for the solution of the second molecule. No twinning was detected by Xtriage. Processing the data in P212121 (Rsym 5.6%, cell 71.3 71.4 228.2 90 90 90) gave me a better molecular replacement solution (LLG 121/373), but I had 5 clashes with the second molecule in the asu. (I tested all alternative spacegroups) I also have a MAD dataset (very low quality!) and I combined the phases with the one obtained from molecular replacement in Sharp. After NCS averaging the maps had improved (still not great). I tried to improve things in the model and run Phaser again and the solution had better statistics (LLG 338/1223) and the clashes were reduced to 2. Xtriage detected pseudo-merohedral twinning with a twin fraction of 43% with twin operator -k, -h, -l. So I tried refining the model with phenix telling it the twinning operator and fraction, but R/Rfree are stuck around 45%. I also tried simulated annealing but that gave even higher R/Rfree. Is there anything I can do, or is it a hopeless case? Thanks for your help in advance! Sabine This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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phenix.refine error
by Jianghai Zhu 12 Sep '07

12 Sep '07

Hi, I was trying the twinning refinement by phenix.refine and I got the following error messages during TLS refinement. Traceback (most recent call last): File "/nfs/home/jzhu/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 "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 81, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1244, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 866, in refinement_machine h_params = h_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ adp_refinement.py", line 175, in __init__ macro_cycle = macro_cycle) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/tls/tools.py", line 600, in __init__ fmodel.info().show_targets(text = prefix+" start model", out = out) AttributeError: 'info' object has no attribute 'show_targets' Could somebody help me? Thanks. Jianghai PS. the version is 2007_08_18_1856. +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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What does mmtbx.twin_map_utils output?
by Francis E Reyes 11 Sep '07

11 Sep '07

Specifically I'm asking about the obs_and_calc.mtz file it produces. 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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So I think I have a twinning problem... ?
by Francis E Reyes 10 Sep '07

10 Sep '07

Hi all The short of the long is that phenix.xtriage on a C2 data set shows twinning with 3 twinning operators (-h,-k-l -k-h-l and k,h,-l). Pushing it through twin_utils, the soution k,h,-l gives an r/rfree of 0.30 and 0.3014 when the twin fraction is 0.352 . The question is where to go from here? I try to phenix.refine the same model in phenix.xtriage (except the mtz file is from the latest round of refinement of that model) and the R/Rfree on macro cycle =2 is 30 and 34 . Unfortunately, it doesn't seem to finish the refinement, I get a seg fault. In the def file for the refinement I set twinning = True and twin_law = k,h,-l . I tried to subject the same model and the .ref file to an autobuild passing in a .eff file for refinement specifying the twin_law, and again I get a segfault / crash when refining the input model. Please advise! --------------------------------------------- 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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Twinning in phenix.autobuild?
by Francis E Reyes 10 Sep '07

10 Sep '07

Hello all So I discovered from xtriage that my crystal is twinned. I have a pretty decent model that xtriage says has an r/rfree of 30/30 to a resolution of 2.6. I wanted to try a phenix.autobuild at 2.8A. I couldn't find a parameter flag for autobuild that turns on twinning. I already autobuilt this model once, and the xtriage log did find that the crystal was twinned, but twinning in refinement of the model during rebuilding wasn't turned on. Is there a way to tell autobuild to rebuild using twinning? 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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crash during refinement with twinned data
by Scott White 10 Sep '07

10 Sep '07

Dear PhenixBB, I'm trying to refine a structure against potentially twinned data. I got the twin law from xtriage. phenix.refine starts, and at some point crashes with the messages below. Refinement proceeds to the end if I don't include twinning. Any suggestions? Thanks, Scott Traceback (most recent call last): File "/software/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/software/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 81, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/software/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1325, in run log = log) File "/software/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 559, in refinement_machine log = log) File "/software/phenix-1.3b/mmtbx/mmtbx/refinement/rigid_body.py", line 347, in __init__ fmodel_copy = fmodel.resolution_filter(d_min = res) File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py", line 1042, in resolution_filter sf_and_grads_accuracy_params = dc.sfg_params File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py", line 890, in __init__ u_part=self.scaling_parameters.u_part ) RuntimeError: cctbx Internal Error: /net/anaconda/scratch1/phenix/phenix-1.3b/cctbx/include/cctbx/xray/f_model.h(91): CCTBX_ASSERT((f_mask.size() == 0) || (hkl.size() == f_mask.size())) failure. -- _______________________________________ Dr Scott A. White Protein Crystallography Group School of Biosciences University of Birmingham B15 2TT E: s.a.white(a)bham.ac.uk T: +44-(0)121-414-7534 F: +44-(0)121-414-5925 W: http://www.bip.bham.ac.uk/cryst ______________________________________

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Re: [phenixbb] Unknown atoms revisitied
by Ralf W. Grosse-Kunstleve 07 Sep '07

07 Sep '07

> Does the atom type have to be a known element or can it something like > element X as seen in some pdb files? > > An example from 1aqn: > HETATM 1951 UNK UNX 277 -4.541 50.540 38.754 0.25 13.93 X > HETATM 1952 UNK UNX 278 -4.443 49.701 37.169 1.00 15.64 X Pavel is correct, but I'll add a some more details. If you want to use these atoms in refinement, you have to decide what scattering type to use. That has to be one of the symbols published in the International Tables for Crystallography, Volume C (see cctbx/eltbx/xray_scattering/it1992.cpp under $PHENIX or cci_app_sources). Regarding the .cif file: data_comp_SIN loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge SIN N N N 0.000 | | | | | this must be a valid "energy type" (see below) | this must be a valid scattering type symbol (Int. Tab.) this can be anything you want mon_lib/ener_lib.cif defines energy types (phenix.where_mon_lib_list_cif shows the path to mon_lib). You can define other energy types in additional .cif files you give to phenix.refine, using the same syntax as in the central ener_lib.cif. Regarding the .pdb file: HETATM 1952 UNK UNX 278 -4.443 49.701 37.169 1.00 15.64 X | | | | this must match the data_comp_UNX | | this must match _chem_comp_atom.type_symbol this must match _chem_comp_atom.atom_id You cannot use X in columns 77-78 because it must match _chem_comp_atom.type_symbol, and that in turn must be a valid scattering type symbol. However, you can leave the column blank. I think I'll change phenix.refine to treat the X like a blank, then you don't have to remove it. But in the current release you have no choice. Ralf

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Re: [phenixbb] Unknown atoms revisitied
by Ralf W. Grosse-Kunstleve 06 Sep '07

06 Sep '07

Hi Jeff, > I was wondering if there were any way to have a single unknown atom > recognized by phenix for refinement. Make up any residue name you like, e.g. SIN (for single N). Create a .cif file like this: data_comp_SIN loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge SIN N N N 0.000 In your PDB file add: ATOM 68 N SIN 15 20.000 20.000 20.000 1.00 20.00 N Add the name of the .cif file to the phenix.refine command line. You can have more than one data_comp_ in the same cif file, if you want to use different element types. Ralf

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