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a question on LSTc refinement
by fn1＠rice.edu 19 Aug '13

19 Aug '13

Hi all, I read some previous post on LSTc [SIA(alpha2-6)GAL(beta1-4)NAG] refinement, but i still cannot figure out how to refine it in PHENIX. In the current version of phenix, i still could not find the ALPHA2-6 link. Does anybody have such experience? Another question is that, sialic acid (SIA) is in the monomer library of phenix. But when i run on the pdb directly, it will give the error information like, "unknown bond type for O1A and O1B". Though this error could be solved by provided the cif file generated by phenix.elbow. Thank you very much! Fengyun

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Ensemble refinement, starting water structure and alternative conformations
by Joseph Noel 19 Aug '13

19 Aug '13

Is it important (or at least useful) to remove any waters before initiating ensemble refinement wherein the waters are located in what is obvious electron density for alternative conformations of side chains? Would the presence of such waters possibly result in ensemble refinement NOT modeling the alternative conformations? ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Density modification using partial model phase
by Yi xing 17 Aug '13

17 Aug '13

Does mtz file from phenix.refine report FOM? If not, is there a way to have FOM listed in the mtz file. I am trying to use the mtz from the phenix refined model as the input of the ccp4 density modification (DM) or Dmmulti. For example, mtz file from Phaser molecular replacement has all the columns to run the DM. Many thanks for any help or comments! Best, yi

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HKL2000 behaved weirdly
by Mengbin Chen 15 Aug '13

15 Aug '13

Dear All, I used HKL2000 to index my data, but weird things happened: after I hit peak search, the data were selected to index, and I chose primitive triclinic to continue. After I hit refine, the circles for peak search disappeared, and if I hit "Bravais Lattice", the table would not show up, which meant that I could not proceed to refine in the potentially correct Bravais Lattice. I don't know if anyone else has encountered this problem before, so any suggestions would be greatly appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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problem with refinement in AutoBuild
by Michael Thompson 15 Aug '13

15 Aug '13

Hello Everyone, I am having a problem running autobuild, which appears to be happening during the refinement step. I start autobuild using : phenix.autobuild data=data.mtz model=model.mtz seq_file=sequence.dat rebuild_from_fragments=True i_ran_seed=124889 find_ncs=False refine_with_ncs=False nproc=4 The runs are failing during the first cycle with the following error message: AutoBuild_build_cycle AutoBuild Run 2 Thu Aug 15 13:37:34 2013 Build cycle 1 of 16 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using NO_LIG_NO_WAT_CloMP_AutoBuild_input_ed.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] No refinement carried out (may need free R flags) Error message from phenix.refine: Refinement failed... Sorry: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_CloMP_AutoBuild_input_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting... /home/miket/projects/CloMP/Oxidized/APSoct2012/CloMP-TMAOcryo_B2_3/MRwithChainsAB/RefineCChalf/AutobuildPrep/AutoBuild_run_2_/LAST.LOG may have additional information... ******************************************************************************** I also checked the LAST.LOG file that is referenced in the error message. That appears to be a phenix.refine logfile, however it just cuts off after the "refinement start" header, with no information about the cause of the failure (no error message). My input MTZ file does indeed contain R-free flags. I have used this MTZ for refinement with phenix.refine (outside of autobuild) with no problems. Furthermore, earlier in the autobuild logfile, I see: Copying refinement_PHX.mtz to exptl_fobs_phases_freeR_flags.mtz Columns used: FP=FP SIGFP=SIGFP FreeR_flag=FreeRflag Which seems to me like it is recognizing my R-free flags column in the input MTZ. Does anyone have any idea what might be going wrong here?? Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Phenix.refine suddenly stopped to refine B-factors
by krimmer＠staff.uni-marburg.de 12 Aug '13

12 Aug '13

Dear all, Phenix.refine suddenly stopped to refine B-factors, even though according to the settings it should refine them (checked box “individual B-factors”). This problem only occurs for one job. The weird thing is that this was always working and I did not do anything different, at least as far as I know. Also, this just happened to a colleague, totally independent from me. We never had this problem before. Here is a part of my log file: |-----overall-----|---macromolecule----|------solvent-------| stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave 0 : 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 The values are not changing at all. The structure is almost done, but it still should change a bit during the refinement cycles. I noticed the problem because I added another water molecule to the structure, and the B-factor stayed at 30.00 which resulted in a negative density blob after refinement. Thank you for your help! Stefan

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How to correct translational psuedosymmetry
by Appu kumar 12 Aug '13

12 Aug '13

Dear all, I have processed a protein-DNA complex data with imosflm. Phenix.xtriage suggest that the is a off origin peak of hight 41.702 hight at fractional coordiantes of 0.500 0.021 0.500 with distance of 40.019 from origin. I am new to such kind of problem, so would you please suggest me how to solve the psuedosymmetry problem encountered in data process. The present unit cells are 55.41 109.72 66.61 90 98.74 90 in space group P1211 with p_value is 3.116e-04. Your help would be much appreciated Thank you Appu

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is phenix trying to polymerize b-octyl glucoside?
by Edward A. Berry 09 Aug '13

09 Aug '13

I'm refining a model with some molecules of the detergent b-octyl glucoside (BOG). I got BOG.cif from a recent ccp4 library, so not sure if this is a suggestion for phenix or ccp4, but: If two BOG molecules are consecutive in the pdb file, phenix stops in setup because it can't find atom HO1 to delete. Even if I had H's in my model there would be no HO1 because O1 is in glycosidic linkage with the octyl chain. I'm guessing phenix somehow realizes there is a sugar and when two are consecutive it autogenerates a link to make a glycosidic bond between them - not appropriate in the case of BOG. easy work around is to intersperse with non-sugar molecules, but if there is a better way, I'll take it. ed RuntimeError: delete_atom_in_place: unknown atom_id: HO1 apply_mod failure: pdbres="BOG R 18 " segid="R " comp id: BOG mod id: DEL-O1 Version: dev Release tag: 1420 Platform: intel-linux-2.6-x86_64 linux

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Ensemble refinement?
by Joseph Noel 08 Aug '13

08 Aug '13

Is anyone having issues executing ensemble refinement in Phenix? I've tried several times now to run things and it always crashes without returning any maps and just returning a set of large PDB files such as: "TEAS-W273E-FPP-A_ensemble_0.6.pdb, TEAS-W273E-FPP-A_ensemble_0.8.pdb, TEAS-W273E-FPP-A_ensemble_0.9.pdb and TEAS-W273E-FPP-A_ensemble_0.1.pdb". The log file always ends with: " Time building chain proxies: 3.01, per 1000 atoms: 0.35 Number of scatterers: 8638 At special positions: 0 Unit cell: (125.75, 125.75, 120.07, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 19 16.00 P 2 15.00 Mg2+ 3 10.00 O 835 8.00 N 717 7.00 C 2765 6.00 H 4297 1.00 sf(0) = scattering factor at diffraction angle 0. AttributeError" I only entering a single chain with solvent and ions and hydrogens. All of the other parameters from the GUI are kept the same. Any suggestions or comments would be much appreciated. Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Restraints file for a modified peptide
by Michael Feldkamp 05 Aug '13

05 Aug '13

I have a peptide that has a fluorescent tag attached to its N-terminus along with a unnatural amino acid incorporated into the sequence. I know how to generate .cif files for the individual ligands using elbow, but I'm at a loss as to get Phenix to recognize these modifications to the peptide so that it refines the structure as one molecule with covalent linkages between the fluorescent tag, peptide and modified amino acid. Any help would be much appreciated. Thanks, Michael

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