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Phenix MTZ files,
by Saba Ferdous 154-FAS/BSBI/F05 01 Jun '11

01 Jun '11

Dear Phenix users I am new to Phenix..probably my question might be childish to you. so with appologies, I have predicted protein structure by using modeller, i want to refine my structure but i am unable to know that what is MTZ files n CIF files because i have only my PDB. And i want to fix beta deviations and outliers, bad angles and bad bonds in my structure. kindly help me and suggest me that what can i do to refine my structure. Best Regards -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan

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ligand cif file
by ChenTiantian 31 May '11

31 May '11

Hi there, Now I use phenix.elbow to produce the cif file of the ligand instead of using Prodrg. but I find a problem with this cif file, the C=N bond is not right, it becomes C-N in the cif file, so it does not fit the electron density, what should I do to modify the cif file to chage C-N to C=N ? Best Regards, Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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mr_rosetta test failure
by Laurie Betts 31 May '11

31 May '11

We installed latest phenix and latest rosetta last week. I ran test script: phenix_regression.wizards.test_command_line_rosetta_quick_tests and got the test failing at the prerefine because of missing shared libraries, as shown below in the FAQ (italics). I tried again in both bash & csh after setting or exporting the environment variables shown below, but got the same exact error. If I do printenv the shell sees the new env var. What should I try next? THanks so much Laurie Betts & CD Poon University of North Carolina *Why does mr_rosetta bomb and say "error while loading shared libraries: libdevel.so: cannot open shared object file: No such file or directory ? This may indicate that somewhere your system is defining the shared libraries that Rosetta needs, and these are for a place that is not where Rosetta expects them to be. You can try to ignore the previous definitions this way: If you are using the bash or sh shells: export PHENIX_TRUST_OTHER_ENV=1 or csh (C-shell): setenv PHENIX_TRUST_OTHER_ENV 1 in the script where you run mr_rosetta, or before you run it from the command line. *

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Re: [phenixbb] strategy suggestion ???
by Michael Thompson 31 May '11

31 May '11

I once used the following strategy to search for ligands when the apo structure had already been determined. I was using Refmac at the time, but I don't see why you couldn't do it with phenix.refine. After you process your data, if your crystals with and without the ligands are isomorphous, then you don't necessarily need to do molecular replacement to get phases. After you process the data from your crystals with the ligands, you can take the mtz file and start refining with the pdb file for your apo structure. You can start with a rigid body refinement to account for any small shifts or rotations that may have taken place when you added the ligand. Then after that refine according to your protocol of choice. The main place you can run into trouble is if you have a polar space group. If you do the rigid body refinement and get a horrible R-factor, the there's a good chance you have indexed the two data sets in opposite orientations. This can be corrected by reindexing, I think the phenix tool for this is xmanip but someone can correct me if I'm wrong. Good luck, Mike ----- Original Message ----- From: "ChenTiantian" <chentiantian2010(a)gmail.com> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Monday, May 30, 2011 6:31:51 PM GMT -08:00 US/Canada Pacific Subject: [phenixbb] strategy suggestion ??? Hi, I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot. Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow: 1, Processing data with XDS (or HKL2000 for some of the datasets) 2,Molecule replacement with phaser. 3,Check and modify the structure residue by residue with COOT, 4,phenix.refine with the following command line: phenix.refine protein.1.mtz protein.pdb \ strategy=individual_sites+individual_sites_real_space+individual_adp+tls \ simulated_annealing=true simulated_annealing.start_temperature=1000 \ simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \ ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \ output.prefix=myprotein 5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. 6,Chage the strategy line to strategy=individual_adp adp.individual.isotropic=all \ to remove the ANISOU lines in pdb file. Any suggestion for this workflow ? or how do you always deal with the similar case ? cause I'm new about this field,maybe I did something stupid. Ps, the value of Rwork and Rfree are too close, like, Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818 Is that reasonable ? -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- 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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strategy suggestion ???
by ChenTiantian 31 May '11

31 May '11

Hi, I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot. Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow: 1, Processing data with XDS (or HKL2000 for some of the datasets) 2,Molecule replacement with phaser. 3,Check and modify the structure residue by residue with COOT, 4,phenix.refine with the following command line: phenix.refine protein.1.mtz protein.pdb \ strategy=individual_sites+individual_sites_real_space+individual_adp+tls \ simulated_annealing=true simulated_annealing.start_temperature=1000 \ simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \ ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \ output.prefix=myprotein 5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. 6,Chage the strategy line to strategy=individual_adp adp.individual.isotropic=all \ to remove the ANISOU lines in pdb file. Any suggestion for this workflow ? or how do you always deal with the similar case ? cause I'm new about this field,maybe I did something stupid. Ps, the value of Rwork and Rfree are too close, like, Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818 Is that reasonable ? -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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Inconsistent R-factors in PDB file
by Schubert, Carsten [PRDUS] 30 May '11

30 May '11

Hi, Not sure if this has been asked before but recently I noticed phenix seems to report inconsistent R-values after each refinement. The final values reported in the screen output after refinement match the values reported in the 'Quick Facts' section, but are not matched by the values in the PDB deposition section. Attached is an example: ... REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS ******************* REMARK Start: r_work = 0.1907 r_free = 0.2151 bonds = 0.004 angles = 0.727 REMARK Final: r_work = 0.1838 r_free = 0.2141 bonds = 0.005 angles = 0.832 REMARK ************************************************************************ ... REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (phenix.refine: 1.7.1_743) REMARK 3 AUTHORS : Adams,Afonine,Chen,Davis,Echols,Gopal, REMARK 3 : Grosse-Kunstleve,Headd,Hung,Immormino,Ioerger,McCoy, REMARK 3 : McKee,Moriarty,Pai,Read,Richardson,Richardson,Romo, REMARK 3 : Sacchettini,Sauter,Smith,Storoni,Terwilliger,Zwart REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.950 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.113 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.33 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.21 REMARK 3 NUMBER OF REFLECTIONS : 29410 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1894 REMARK 3 R VALUE (WORKING SET) : 0.1877 REMARK 3 FREE R VALUE : 0.2122 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.74 REMARK 3 FREE R VALUE TEST SET COUNT : 1982 For regular work I really don't care as long as the values are consistent and tell me if the refinement reached convergence, but for a deposition it matters a bit more. So which values should I report for a paper? Cheers, Carsten

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Iterative build composite omit hanging
by José Trincão 30 May '11

30 May '11

Hello, I tried to run an iterative build composite omit for my protein - P1, 1350 residues/monomer, 4 molecules in the A.U.. After about 1.5 weeks running almost all was done except one omit region which was stuck. I had two processes running indefinitely (reduce and python) with no output. I tried to rerun that region alone but it gets stuck also with reduce producing no output. What should I do to get the complete map (I am going to merge all the other regions together, but would like to know why this particular one is problematic). Thanks! Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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isotropic
by ChenTiantian 30 May '11

30 May '11

-- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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sigmaA-weigted 2FoFc maps by only mtz file
by zhangh1＠umbc.edu 28 May '11

28 May '11

Hi, If I only provide a mtz file with Fo, Fc and phase data, and do NOT have the pdb file, can any phenix utility calculate the sigmaA-weigted 2FoFc maps? Thanks! Hailaing

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SA omit map for ligand
by Tjaard Pijning 27 May '11

27 May '11

Hi, I am trying to make an SA-omit Fo-Fc map for a sugar ligand (chain B) bound to protein (structure solved by MR), without doing any rebuilding of protein or ligand – just calculate an Fo-Fc map that I can load into PyMol. So far I used the AutoBuild – Create omit map module with these settings : - input files : model (protein+ligand+waters), data (.mtz), restraints for sugar ligand (.cif) - omit map type : simulated annealing - omit region : omit selection - omit map options : keep input waters, omit chain list : omit_chain_list chainB However, the ligand gets modified even though I use “omit_chain_list chainB”. What are the parameters to set to keep the model (protein, ligand, waters) from being rebuilt ? Furthermore, what is the procedure to load the SA Fo-Fc omit map into pymol ? Phenix version is 1.6.4-486. Thanks in advance, Tjaard Ing. Tjaard Pijning Research Assistant Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85

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