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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 27 May '11

27 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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get_cc_mtz_pdb results
by Jerome Nwachukwu 27 May '11

27 May '11

Hi: I am using get_cc_mtz_pdb to compare some structural models and found differences in overall CC around ~0.0056 and local CC around 0.0033. How much difference in local and overall CC values between two models is generally considered significant? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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a new PDB clustering tool available in phenix from nightly build dev-756
by Francois Berenger 26 May '11

26 May '11

Dear Phenix users, Starting from the nightly build dev-756, a new clustering tool called DURANDAL is included in Phenix. It performs exact clustering of proteins in PDB format, fast. It is primarily aimed at people working in protein structure prediction and having to deal with a lot of protein models. The correspondence used to compute CARMSD for a pair of proteins is 1 to 1. If two proteins A and B are to be optimally superposed, both PDB files (A.pdb and B.pdb) must have the same numbers of alpha carbons. The first alpha carbon in A.pdb will be matched to the first alpha carbon in B.pdb, and so on. Clustering up to 20,000 PDB files should work on most machines. Workstations with a lot of memory will be able to cluster even more files. Examples: --------- * to perform exact clustering using a fixed cutoff value of 3.0 Angstroms: durandal.cluster_pdbs -i [file_containing_one_PDB_filename_per_line]\ -d 3.0 -o out -s -v * there is also another tool included, to compute CARMSD of many files versus a reference one (the first in the list is considered the reference): durandal.rank_pdbs [file_containing_one_PDB_filename_per_line] If you want to know more about how the software is working, you can have a look at http://bioinformatics.oxfordjournals.org/content/27/7/939 Don't hesitate to ask if you encounter any problem while using the software. Best regards, Francois Berenger.

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ADP refinement
by Christian Roth 26 May '11

26 May '11

Dear all, I am sorry for this very stupid question, but I probably overlooked the relevant text in the documentation. I requested the refinement of a heavy atom (chloride) with anisotropic ADP. In the log than isotropic refined ADP were set for 0 atoms. I guess I have to define all other chains as isotropic. Is that right. I have a lot of chains, it would be possible but a pain (more than 40 chains). Is there a something like refine anisotropic chain x and all others isotropic? Thanks and best Regards Christian

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Quick PHENIX install question
by Yuri 26 May '11

26 May '11

Hello PHENIXers, I just got a computer with Red Hat workstation 5 running 64-bit architecture. Which build should I install? Thank you -- Yuri Pompeu

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