November 2013 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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Postdoc positions (SGC, Diamond): fragments into crystals
by Frank von Delft 02 Jan '14

02 Jan '14

Hello, I have 3 open postdoc positions, to work on technologies around fragment screening in crystals, which is what my (joint) research team at Diamond (beamline I04-1) and SGC (PX group) is trying to make simple and accessible. Details of the project are on my website <http://www.thesgc.org/scientists/groups/oxford/crystallography>; we need smart people to: * (at SGC) test-drive with start-to-end soaking campaigns <http://www.thesgc.org/careers/oxford/crystallography-postdoc-fragment-scree…> * (at SGC) develop crystal engineering to get soakable systems (molecular biology, biochemistry) <http://www.thesgc.org/careers/oxford/crystallography-postdoc-crystal-engine…> * (at Diamond) explore soaking techniques <http://www.diamond.ac.uk/Home/Jobs/Current/DIA0886_CH.html> The application deadlines for the SGC posts are a function of the UK's charming political climate; if you're interested but from outside the EU, alert me with a direct email plus CV. phx. P.S. if you know smart undergrads who'd be interested in a DPhil in that sort of thing -- applied engineering, technology -- send them to that website too. (DPhils are what you get in Oxford - that makes it special. Or "special".)

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Submissions for next CCN newsletter
by Nigel Moriarty 06 Dec '13

06 Dec '13

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2014 issue is 15 December 2013 but if you can send me an email we can make exceptions so you can use the holiday break to work on your drafts. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Red patches of electron density
by Singh, Bishal 02 Dec '13

02 Dec '13

Hi, I am solving a crystal structure at 1.2 Å with completeness 97.3% in the highest resolution shell. There are few small patches of red electron densities on the main chain of a flexible loop at a contour level of ~3sigma of difference ED map. Refinement parameters were following: XYZ coordinates, individual B-factor, optimize X-ray/stereochemistry weight, optimize X-ray/ADP weight and individual Anisotropic ADP for amino acids excluding hydrogen. Target weights are as default in phenix.refine. I already have observed two alternative conformation for this region in another crystal structure. Therefore I am thinking that these red patches are because of lower occupancy of these residues. Please suggest me what shall I do. I shall be grateful for your words. With regards, Bishal Singh University of Heidelberg, Germany

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Iterative build omit map error
by Heather L Condurso 27 Nov '13

27 Nov '13

SO just as my omit map run should have finished, it gave an error instead. I'm running 1.8.4-1496 on a Mac with OSX 10.6.8 and 8GB of memory. Here is the end of the log file: Splitting work into 32 jobs and running with 1 processors using sh background=False in /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_3.log Starting job 4...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_4.log Starting job 5...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_5.log Starting job 6...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_6.log Starting job 7...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_7.log Starting job 8...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_8.log Starting job 9...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_9.log Starting job 10...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_10.log Starting job 11...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_11.log Starting job 12...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_12.log Starting job 13...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_13.log Starting job 14...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_14.log Starting job 15...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_15.log Starting job 16...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_16.log Starting job 17...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_17.log Starting job 18...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_18.log Starting job 19...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_19.log Starting job 20...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_20.log Starting job 21...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_21.log Starting job 22...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_22.log Starting job 23...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_23.log Starting job 24...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_24.log Starting job 25...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_25.log Starting job 26...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_26.log Starting job 27...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_27.log Starting job 28...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_28.log Starting job 29...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_29.log Starting job 30...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_30.log Starting job 31...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_31.log Starting job 32...Log will be: /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log : /TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz Rebuilding side chains from Build_composite_refined_3.pdb Refining model: edit_model.pdb approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.0197876048373 approx_equal ERROR 0.0197856373852 approx_equal ERROR Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /Users/stevebruner/Desktop/APS_102313/MdnJB/AutoBuild_run_22_/TEMP0/RUN_FILE_32.log : /TEMP0/Build_composite_refined_3.pdb R/Rfree=0.32/0.39 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz Rebuilding side chains from Build_composite_refined_3.pdb Refining model: edit_model.pdb approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.0197876048373 approx_equal ERROR 0.0197856373852 approx_equal ERROR Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz to AutoBuild_run_32_/TEMP0/refine_fmodel.mtz Moving refinement file AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3_001.mtz to AutoBuild_run_32_/TEMP0/refine_map_coeffs_3.mtz Model: AutoBuild_run_32_/TEMP0/Build_composite_refined_side_3.pdb R/Rfree=0.33/0.38 Maps from refinement will be filled (2FOFCWT PH2FOFCWT) Set refine map coeffs file pdb_file_refine_map_coeffs to refine_map_coeffs_3.mtz ******************************************************************************** Can this be salvaged? It took 5 days to run. I found a section about this in the documentation, but I can't find the maps for each region overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. I can only find working_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc. Will these maps work? Can you tell what the error means so that I can avoid this problem in the future? Thanks, Heather

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zero B-factors
by Edna Patricia Matta, Ms 26 Nov '13

26 Nov '13

Hello, Recently I did submit a structure to the PDB but they found that some atoms had zero value for the B-factors. I am new in this filed and I do not know what to do. There have been reports of problems with some versions of phenix about this. I used Phenix 1.8. I repeted the refinement doing restrain NCS-related B-factors but I do not find where to check for the the B-factor values in the the log file. Somebody can help me? Thanks a lot, Edna

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Re: [phenixbb] [ccp4bb] Ligandfit - problem with ligand_start
by Terwilliger, Thomas C 25 Nov '13

25 Nov '13

Hi Danilo, The most likely problem is that the ligand_start file has to have enough atoms in it to define a fixed group in the ligand. The way that ligandfit works is that it breaks a ligand up into rigid groups connected by rotatable bonds. The ligand_start file has to contain one complete rigid group. So probably if you supply a little more of the ligand then it might run. Just to test this, can you try this test of using a ligand_start file: phenix_regression.wizards.test_resolve resolve test_fit_start And then if that gives an "OK", try this: cd test_fit_start phenix.ligandfit ligand=side.pdb ligand_start=start.pdb resolve_map.mtz quick=true Does that run? If you the look at LigandFit_run_1_/TEMP0/resolve_ligand_fit.log Does that say >ligand_start start.pdb Starting configuration of ligand will be read from: start.pdb If all that works, then try adding more atoms to your ligand_start file. Let me know if that doesn't do it! All the best, Tom T Dear all, I am working on a membrane protein covalently bound to a molecular antanna: it is known that this molecule binds to lysine residue but I do not know how many and which lysine residues it binds. 20 diffraction datasets of this protein-ligand complex have been obtained and now, I would quickly localize the ligand using the Fo-Fc map of each data set and using the information on the covalent bound protein-ligand. Ligandfit tool (PHENIX) seems to be indicated to do this; to use the information on the covalent bound, I am using the ligand_start keyword with a pdb containing a ghost atom (however present in ligand model) perfectly superposed to the lysine atom that should bind the ligand. The command used is: phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \ refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif description: - prot.mtz (data) - prot.pdb (protein without ligand) - lig.pdb (ligand containing ghost atom) - lig_start.pdb (ghost atom superpose to NZ of a lysine) - lig.cif (restrain of lig.pdb) Strangely, no ligand is found at the end of the process even reducing ligand_cc_min to 0.01. I have run the same command by using an other protein where an other ligand has been correctly fitted but, also in this case, no ligand has been detected. Conversely, without the use of ligand_start, ligandfit properly localizes the ligand. I'm doing some mistake in the use of ligand_start? Do you know an other tool to perform a ligand fitting in these conditions? Thanks for your answers. Danilo

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Ligandfit - problem with ligand_start
by Danilo Belviso 25 Nov '13

25 Nov '13

Dear all, I am working on a membrane protein bound to a antenna molecule: I know that the molecule binds to lysine residue but I do not know how many and which lysine residues it binds. 20 diffraction datasets of protein-ligand complex have been obtained and now, I would quickly localize the ligand using the Fo-Fc map of each data set and using the information on the covalent bound protein-ligand. Ligandfit tool (PHENIX) seems to be indicated to do this; to use the information on the covalent bound, I have thought to use the ligand_start keyword with a pdb containing a ghost atom (however present in ligand model) perfectly superposed to the lysine atom that should bind the ligand. The command used is: phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \ refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif description: - prot.mtz (data) - prot.pdb (protein without ligand) - lig.pdb (ligand containing ghost atom) - lig_start.pdb (ghost atom superpose to NZ of a lysine) - lig.cif (restrain of lig.pdb) At the end of the processing, ligand is not found. So, I have tryed with ligand_cc_min=0.01, but also in this case ligandfit does not give result. I have thought that no ligand is present. However, to be sure that all was correct, I have run the same command by using an other protein where an other ligand has been correctly fitted. Also in this case, no result has been obtained. Conversely, without the use of ligand_start, ligandfit properly localizes the ligand. I'm doing some mistake in the use of ligand_start? Thanks for your answers. Danilo

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using reference model with polyA chain.
by Francis Reyes 20 Nov '13

20 Nov '13

I'm refining a structure ( at low res ), so I trimmed off all the side chain atoms from my model while my reference model still has these chains. I'm receiving errors like... ----------Correcting rotamer outliers to match reference model---------- ** evaluating rotamers for working model ** A 502 ILE is missing some sidechain atoms, **skipping** A 504 LYS is missing some sidechain atoms, **skipping** A 505 VAL is missing some sidechain atoms, **skipping** I don't care about the side chain atoms, but I'd still like the reference model restraints to provide secondary structure. Does "**skipping**" mean that the reference model is no longer being considered for the particular residue? Or will I still retain my secondary structure from the reference model? Thanks, F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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completeness problem in phenix.refine
by Yarrow Madrona 19 Nov '13

19 Nov '13

Hi, I recently merged two data sets, one having a phase and the other Amplitudes. For some reason my completeness is always 50%. I had anomalous data but the completeness is around 100% after processing and when I do an mtz dump. I'm confused why I get a completeness of 50%. Thank you for any help you can provide. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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