May 2008 - phenixbb - phenix-online.org

Shell variable SSH_Path not set
by shivesh kumar 23 May '08

23 May '08

Dear all, We have installed Phenix in Red Hat Linux enterprises 5. It takes a long time for the GUI to appear with the following message-- Shell variable SSH_Path not set What is the solution of this problem. Thanx in advance for suggestions. shivesh

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NCS restraints
by Rife, Christopher L 22 May '08

22 May '08

I'm refining a twinned structure at 2.2A that has 6 copies in the ASU. I am using NCS, however the ncs restraints are so tight that they are keeping the chains identical even though this takes them out of the density. Are there any parameters I can adjust that will lessen the strength of these restraints? Taking away NCS completely is also not ideal. I guess I would like an equivalent of 'medium' or 'loose' NCS restraints as implemented in Refmac. Thanks, Chris

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Re: [phenixbb] Any real space map-mask / NCS utility?
by Tom Terwilliger 22 May '08

22 May '08

Hi Partha, I think we don't have a tool for just what you want...but here is an idea given what you are trying: In coot build a short piece of polypeptide in the region where one ha site is located. Match the map in some way. Now rotate/translate this exact piece of chain over to your other sites and match the density there. Now use phenix.superpose_pdbs to find your ncs and put that in resolve. Good luck! -Tom t At 05:48 AM 5/22/2008, you wrote: >Hi, > >Apologies for the strange question. > >Since phenix has one fantastic tool for each kind of purpose, I was >wondering if there is something that could combine features of USF >Rave package for example.. basically the question arises from the >difficulty of finding NCS operators in some cases, if we have less >than three heavy atoms per molecule or map is too bad to build >something. > >I am trying to create a mask around a heavy atom site in the map, give >it a translation to the next heavy atom which is probably in the next >molecule, give a 6d rotation and use that in Resolve for NCS >averaging. > >Any suggestion / script would be greatly appreciated. > >Cheers, Partha > > >-- >MRC National Institute for Medical Research >Division of Molecular Structure >The Ridgeway, NW7 1AA, UK >Email: pchakra(a)nimr.mrc.ac.uk >Phone: + 44 208 816 2515 >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Any real space map-mask / NCS utility?
by Partha Chakrabarti 22 May '08

22 May '08

Hi, Apologies for the strange question. Since phenix has one fantastic tool for each kind of purpose, I was wondering if there is something that could combine features of USF Rave package for example.. basically the question arises from the difficulty of finding NCS operators in some cases, if we have less than three heavy atoms per molecule or map is too bad to build something. I am trying to create a mask around a heavy atom site in the map, give it a translation to the next heavy atom which is probably in the next molecule, give a 6d rotation and use that in Resolve for NCS averaging. Any suggestion / script would be greatly appreciated. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

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decrease number of refs in test set
by Mark A Saper 22 May '08

22 May '08

I have a data set with about 10% of the reflections in the test set. I want to retain this test set for further refinement in phenix, but I want to decrease the number of reflections to say 5%. Can this be done in phenix? Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor, Biophysics and Department of Biological Chemistry University of Michigan 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 Research summary

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phenix.twin_map_utils gives AttributeError: 'module' object has no attribute 'r_free_flags_params'
by Francis E Reyes 21 May '08

21 May '08

chem171-152-dhcp:exptl_fobs_phases_freeR_flags.mtz francisreyes$ phenix.twin_map_utils xray_data.file=exptl_fobs_phases_freeR_flags.mtz model=MR.1_pdbset1_refine_007.pdb unit_cell=73.5,73.5,114,90,90,90 space_group="P 41 21 2" twin_utils { input { unit_cell = 73.5 73.5 114 90 90 90 space_group = "P 41 21 2" xray_data { file_name = "exptl_fobs_phases_freeR_flags.mtz" obs_labels = None free_flag = None } model { file_name = "MR.1_pdbset1_refine_007.pdb" } } parameters { twinning { twin_law = None max_delta = 3 } } output { logfile = "twin_tools.log" map_coeffs_root = "MAP_COEFFS" obs_and_calc = "obs_and_calc.mtz" } } Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/command_line/ twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/twinning/ twin_map_utils.py", line 256, in run tmp_params = utils.r_free_flags_params.extract() AttributeError: 'module' object has no attribute 'r_free_flags_params' 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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phaser_x.mtz, resolve_x.mtz and exptl_fobs_phases_freeR_flags.mtz give different Rfree's using same model?
by Francis E Reyes 20 May '08

20 May '08

Ok. I think I have a case where I can't refine unless I use density modified experimental phases. I did an autosol run where I specified build=False so I don't have an exptl_fobs_phases_freeR_flags.mtz, but I do have phaser_1.mtz and resolve_1.mtz. However, when I refine my model using mlhl my Rfree drops below 30 when using resolve_x.mtz and not phaser_x.mtz nor using the original d*trek ref using the same model? Using any of the other mtz's results in Rfree's in the mid 30s. Interestingly refining against the original d*trek results in an increase of Rfree with macro cycle? I checked the log file for resolve_x.mtz and although it says it's using the mlhl refinement target, it seems to be using FP, SIGFP (not the HL coefficients that I thought phased refinement would use) as evidenced by the .log file under 'Non-default parameters'. In this section it doesn't read in the HL cofficients? Is there any indication that it's actually refining against the phases? Any insight as to which mtz to use for final refinement would be suggested. Thanks FR P.S. What is the refinement target ml_sad? --------------------------------------------- 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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problem with high Rfree
by Christina Bourne 20 May '08

20 May '08

Hello BB, I am working on a structure that is twinned (merohedral) in P41. Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far). My MR soln is good (Phaser LLG ~550) with 4 mols per AU; this gives good packing with no room for another mol. I have data from 48-2.8A. I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension. During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from Xprep the data looks OK. (Yes, I am trying to grow different forms) Maps look nice, although I wish my ligand had more/better density. I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true. My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270. Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong. Why is my Rfree hanging so high? Is it becaues I have bad karma? Is it to do with the twinning? I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43). There isn't room for anything else in the cell. Any opinions or suggestions are most welcome as I wait for better xtals to grow... Thanks in advance, Christina

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Can't autobuild after autosol?
by Francis E Reyes 19 May '08

19 May '08

******************************************************************************** Failed to carry out AutoBuild_start: Sorry, 'after_autosol' is set, but there were not any solutions from AutoSol found...please make sure that the highest-numbered AutoSol run is a completed run (you can use 'phenix.autosol show_runs' to see what runs are present and 'phenix.autosol delete_runs=xx' to remove any incomplete runs) ******************************************************************************** when issues with phenix.autobuild after_autosol phenix.autosol show_runs gives.. ------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol display_runs=True --------------------------------------------------------------------------- List of runs for AutoSol Run Title / Notes --------------------------------------------------------------------------- --------------------------------------------------------------------------- 3: Run 3 AutoSol Fri May 16 13:10:11 2008 STEP: finished Top solution: # 2 Dataset #1 Score: 27.84 FOM: 0.29 Built: 121 Side-chains: 0 Chains: 21 CC: 0.45 Sites: 4 Score type: CC RFACTOR SKEW FOM NCS_OVERLAP Raw scores: 0.61 0.59 0.03 0.30 0.00 Z-scores: 14.84 5.76 1.26 5.98 0.00 --------------------------------------------------------------------------- Does that mean an autosol run has completed? 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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Tell phenix.autosol to find more heavy atoms?
by Francis E Reyes 19 May '08

19 May '08

I have a SAD map which is beautiful, but I want to look for more heavy atoms before further refinement... Would the proper procedure be.... SAD dataset, reading heavy-atom sites from a PDB file written by phenix.hyss: phenix.autosol 11 Pb data=deriv.sca seq_file=seq.dat \ sites_file=deriv_hyss_consensus_model.pdb This will carry out the usual structure solution process, but will read sites from deriv_hyss_consensus_model.pdb, try both hands, and carry on from there. If you know the hand of the substructure, you can fix it with have_hand=True. Would there be a PDS friendly way to do this (not necessary though) ? i.e. phenix.autobuild after_autosol --------------------------------------------- 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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