- phenixbb - phenix-online.org

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 01 Jun '11

01 Jun '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 01 Jun '11

01 Jun '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 01 Jun '11

01 Jun '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 01 Jun '11

01 Jun '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] 31 May '11

31 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 28 May '11

28 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 27 May '11

27 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 27 May '11

27 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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Equations of transformation
by Hena Dutta 26 May '11

26 May '11

Dear Members, Sorry, if my question is out of the field. I want to know the mathematical relations between 2 sets of co-ordinates, one before and one after the rotation. I used COOT to rotate the side chain (containing atoms N1, C2, N3, C4, C5, C6, N6, N7 and C8) of Adenine by 180 degree about the glycosidic bond (C1’-N9). How the initial co-ordinates (Xi, Yi, Zi) and final co-ordinates (Xf, Yf, Zf) are mathematically related? I shall be very grateful if someone can tell me the equations. Regards... Hena

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Refining sucrose
by Priit Eek 23 May '11

23 May '11

Hi, I couldn't find this (probably basic knowledge) in the manual or here, so... I have a problem with refining a sucrose ligand. It is not covalently bound to the protein – just electrostatic interaction. The density isn't the best, but it's still obvious it must be there. LigandFit can find the blob and fits the sucrose in there quite well, but when I run phenix.refine it distorts the geometry of the molecule and complains about it later in MolProbity - Basic Geometry validation in almost every possible way. How can I apply more stringent restraints to the ligand so its geometry wouldn't get so twisted? This might not be the most appropriate list for my second question, but the problem is the same and somebody probably knows: how to manually modify that sucrose in Coot (eg rotate only one ring or a -CH2OH group) or perform real space refinement? Right now I can only rotate/translate the whole sucrose and trying to perform a real space refinement results in an error ("Failed to match (to the dictionary) the following model atom names: SUC C1 C2 C3 C4 C5 C6 O1 O2 O3 O4 O6. That would cause exploding atoms, so the refinement didn't start.") I haven't specified any custom cif libraries as SUC should be present in the built-in library of both Phenix and Coot. I'm using Phenix v1.7.1-743 and Coot v0.6.2-pre-1-rev3450 on OS X 10.6.7. Thank you in advance! Regards, Priit Eek

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Call for articles and short communications for Computational Crystallography Newsletter
by Nigel Moriarty 23 May '11

23 May '11

Dear Colleagues I'm accepting short communications and articles of general interest to crystallographers working on macromolecular systems for the next issue of the Computational Crystallography Newsletter. You can see recent issues at http://www.phenix-online.org/newsletter/ as well as the word template for article submission. The deadline is June 17th but early submission is appreciated. Nigel -- Nigel W. Moriarty, PhD 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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Weird R-free discrepancy.
by Yuri 22 May '11

22 May '11

I was working on a model for at 1.9 A using the previous phenix release (650). I was almost finished r-free was 0.197. I installed the newest release and refined again and my r-free went up to 0.228!!. The values for bsol and ksol look significantly different. I do not understand where the biggest difference is coming from... Below I pasted part of the .log files. Old and new, respectively. =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.90 - 28.74 A; n_refl. = 32203)------------------------------| | | | r_work= 0.1747 r_free= 0.1967 ksol= 0.40 Bsol= 39.70 scale= 0.064 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-1.65,-1.65,3.31,-0.00,0.00,0.00); trace/3= -0.00 | | | | maximum likelihood estimate for coordinate error: 0.21 A | | x-ray target function (ml) for work reflections: 2.567485 | =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.90 - 28.74 A; n_refl. = 34277)------------------------------| | | | r_work= 0.1911 r_free= 0.2279 ksol= 0.40 Bsol= 59.62 scale= 0.063 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-1.73,-1.73,3.47,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.55 A | | x-ray target function (ml) for work reflections: 2.591014 | |-----------------------------------------------------------------------------| -- Yuri Pompeu

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BRU error
by Krystle Williams McLaughlin 21 May '11

21 May '11

Hi, I'm using phenix for refinement and I keep getting an error. My DNA strand has a bromo-uridine in it and phenix.refine keeps crashing on this nucleotide. Here is the error: Number of atoms with unknown nonbonded energy type symbols: 40 "ATOM 2770 P BRU P 5 .*. P " "ATOM 2771 O1P BRU P 5 .*. O " "ATOM 2772 O2P BRU P 5 .*. O " "ATOM 2773 O5* BRU P 5 .*. O " "ATOM 2774 C5* BRU P 5 .*. C " "ATOM 2775 C4* BRU P 5 .*. C " "ATOM 2776 O4* BRU P 5 .*. O " "ATOM 2777 C1* BRU P 5 .*. C " "ATOM 2778 N1 BRU P 5 .*. N " "ATOM 2779 C6 BRU P 5 .*. C " ... (remaining 30 not shown) Here is what I have in my pdb: ATOM 2901 P BRU E 5 33.977 -16.324 24.303 1.00 27.21 P ATOM 2902 O1P BRU E 5 34.027 -15.724 22.919 1.00 28.22 O ATOM 2903 O2P BRU E 5 33.857 -15.340 25.393 1.00 25.06 O ATOM 2904 O5* BRU E 5 32.721 -17.236 24.418 1.00 28.02 O ATOM 2905 C5* BRU E 5 32.487 -18.228 23.495 1.00 28.50 C ATOM 2906 C4* BRU E 5 31.047 -18.347 23.082 1.00 32.59 C ATOM 2907 O4* BRU E 5 30.337 -18.858 24.152 1.00 28.61 O ATOM 2908 C1* BRU E 5 29.369 -17.891 24.535 1.00 29.63 C ATOM 2909 N1 BRU E 5 29.279 -17.855 25.962 1.00 29.72 N ATOM 2910 C6 BRU E 5 30.426 -17.755 26.799 1.00 30.57 C ATOM 2911 C5 BRU E 5 30.251 -17.738 28.232 1.00 30.89 C ATOM 2912 BR BRU E 5 31.869 -17.591 29.321 1.00 57.08 Br ATOM 2913 C4 BRU E 5 28.917 -17.845 28.826 1.00 30.70 C ATOM 2914 O4 BRU E 5 28.768 -17.825 30.033 1.00 29.36 O ATOM 2915 N3 BRU E 5 27.785 -17.945 27.981 1.00 29.36 N ATOM 2916 C2 BRU E 5 27.961 -17.966 26.552 1.00 29.05 C ATOM 2917 O2 BRU E 5 26.994 -18.064 25.848 1.00 35.29 O ATOM 2918 C3* BRU E 5 30.464 -17.006 22.751 1.00 34.58 C ATOM 2919 C2* BRU E 5 29.845 -16.605 23.968 1.00 33.10 C ATOM 2920 O3* BRU E 5 29.526 -17.213 21.768 1.00 37.93 O I have already run a BRU molecule through ReadySet and when I use the cif file generated from this phenix.refine will run through but when the Bromine atom is in the structure has a large negative density peak in the Fo-Fc map. I think it may just be a naming thing. BRU is already in the monomer library so I don't understand why I get an error at first also without the readyset cif file. Any suggestions? Thanks, Krystle

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Phenix 1.7 with Rosetta and PBS/Torque
by Jeremy Mann 20 May '11

20 May '11

Reading the documentation is is unclear with queue system will work with Phenix 1.7. qsub is mentioned but not referred as the qsub from Torque/PBS or qsub from Grid Engine. Which qsub are the developers referring to? -- Jeremy Mann jeremy(a)biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 767-3419 ^^^^^^^^ ** NEW OFFICE NUMBER **

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map error?
by Christian Roth 20 May '11

20 May '11

Dear all, I got a error message in the last round of phenix.refine which seesm to be related to map or mtz file creation (error.txt attached). I used the GUI and I unchecked the map creation option in ccp4 or Xplor before I started the run. I am not sure whats going wrong here. Please could you point me to the problem. Best regards Christian

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AutoSol
by Nora Cronin 20 May '11

20 May '11

Whilst I can input SAD SAD data ie two different SAD datasets using Group =1 and Group =2 with the "Wavelength" keyword, how do I input 2 different crystals using the "crystal_info" keyword which does not recognize Group = Inputting .sca unmerged anomalous data how do I input data for 2 different crystal_info keywords with different heavy atoms and different unit cells? thanks Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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mr_rosetta on a supercomputer
by Patricia Amara 18 May '11

18 May '11

Hello, I have been trying to run phenix.mr_rosetta on a supercomputer where we are limited to 24h for parallel jobs and we have different queues for job mono. Thus to run we have two files. We do not really understand how the code proceeds with nproc so we just put 6 for now. When we sent it, it created 1000 jobs on MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 it sent 10 jobs mono, but ran only 5 first than the other five. Then the job running the script hangs. when we looked at the log files in the MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 directories it filled up only 4 if we re-run only 3 and never the same. do you have any idea what we're doing wrong? thanks in advance for your input Patricia Amara ps; Thus to run we have two files. One to send the script #!/bin/bash #MSUB -e ros1_%I.e #MSUB -o ros1_%I.o #MSUB -n 6 #MSUB -T 86400 cd /scratch/cont003/amara/Rosetta-NadA ./rosetta.run and the script itself: phenix.mr_rosetta \ seq_file=/scratch/cont003/amara/Rosetta-NadA/NADA.seq \ data=/scratch/cont003/amara/Rosetta-NadA/NadA-7-BM16-remote-no_ano-P21212-Rfree_shell.mtz \ search_models=/scratch/cont003/amara/Rosetta-NadA/model_2.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = /scratch/cont003/amara/Rosetta-NadA/aat000_03_05.200_v1_3.gz \ fragment_files = /scratch/cont003/amara/Rosetta-NadA/aat000_09_05.200_v1_3.gz \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=3 \ space_group=p21212 \ use_all_plausible_sg=False \ max_wait_time=100 \ nproc=6 \ group_run_command= "/usr/share/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/bsub -n 1 -q mono -W 03:00"

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phenix.model_vs_data enhancement request
by Schubert, Carsten [PRDUS] 18 May '11

18 May '11

Hi Pavel, do you think it would be possible to extend the statistics printed out by phenix.model_vs_data, so it also does a break-down by chains? Right now the stats are listed by residue type, i.e. protein/ligand/solvent/etc. For instance if I am interested in the B-factors of a glycosylated protein with ligands, the sugars and ligands all get muddled together. Breaking this down by chains as well would allow for finer control. Cheers, Carsten

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Polygon graphs
by Tanner, John J. 18 May '11

18 May '11

Does anyone know whether the polygon graphs from the following paper were ever incorporated into phenix? Crystallographic model quality at a glance Acta Crystallogr D Biol Crystallogr. 2009 March 1; 65(Pt 3): 297300. -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tannerjj(a)missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html

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Phenix Refine
by Thomas C. Terwilliger 17 May '11

17 May '11

Hi Haytham, This means that you have two atoms in your pdb file that both have the name BR PDB F 1 You can find these with: grep 'BR' my_pdb_file.pdb |grep BR Let me know if that doesn't do it! All the best, Tom T >> when i refine using phenix.refine i get this error >> >> number of groups of duplicate atom labels:1 >> total number of affected atoms: 2 >> group "HETATM 3466 BR PDB F 1 .*. BR " "HETATM 3467 BR PDB F 1 .*. BR " >> >> could you please tell me what is that >> >> Haytham Wahba >> PhD stu >> UdeM >> >>

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Postdoctoral positions in structural biology
by Protein Crystallography 16 May '11

16 May '11

Postdoctoral positions are available immediately in the *Structural Biology Laboratory* headed by *Dr. C. S. Raman* at the University of Maryland, Baltimore. Research in the Raman laboratory combines structural, biophysical, biochemical, and cell biological approaches to understand the molecular mechanisms underlying cellular signaling. The laboratory is equipped with state-of-the-art equipment for fermentation, high-throughput protein expression, purification, crystallization (liquid handlers for screen generation and optimization, Mosquito LCP robot, and crystal imaging systems), X-ray diffraction, and high definition mass spectrometry (Synapt G2 HDMS). In addition, we have ready access to synchrotron facilities. For a representative example of our work, please consult*:* *Nature 455: 363-368*. Applicants should hold a PhD in biochemistry, biophysics, chemistry, molecular biology, or a closely related field. Applicants should have experience in protein crystallography as well as a good publication record. Strong background in protein expression and biophysical characterization is essential. Expertise in membrane protein purification is a plus. Furthermore, strong communication skills in oral and written English are required. To apply, please, send a letter of interest, a CV, and names of three references by e-mail to: craman(a)rx.umaryland.edu

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missing/extra atoms in phenix.refine
by R.M. Garavito 13 May '11

13 May '11

We are trying to finish up the refinement on two structures, but we have run into a strange problem that I have never seen before. So we need to ask the Phenix experts. As background, we recently solved the structure of an 808 residue enzyme, which crystallizes as a tetramer. In the asymmetric unit there are two tetramers (>6400 residues, ~52,000 atoms, but 67% solvent). After SAD phasing and autobuild (many kudos to the Phenix team), we were able to trace easily the chain in two different ligand complexes, one at 2.85 Å and the other at 2.8 Å. Although the C-terminal domains are quite well resolved (and obey 222 NCS), the first domain (~110 residues out of 808) is a bit disordered and shows some conformational differences between each monomer. While the main chain in this domain can be traced, side chain densities are mediocre to missing in spots. In order to ensure a consistent tracing and sequence assignment between all 8 N-terminal domain, we built in the "correct" sequence, but truncated the side chains to CB if the side chain density was poor to non-existent. After several rounds of refinement and model building, the finished structures look quite good, have a consistent sequence assignment, and have Rwork in the high teens and Rfree in the low 20s. THE PROBLEM: It is the 2.8 Å complex that has the problem. We used Moleman2 to evaluate the B-factors for the 4 domains in the 8 monomers in the ASU. When we compiled the numbers, we noticed that Moleman2 and phenix.refine gave different numbers for the protein atoms for chain B in the 2.8 Å complex (6152 versus 6289). We checked the PDB and confirmed that there are 6152 protein atoms in chain B; the other 7 chains show no differences between the programs. So where did phenix.refine get 6289 protein atoms when only 6152 protein atoms are input for chain B? The number of residues are correct (780). Adding to the confusion, there are truncated residues in each of the 8 chains. In the phenix.refine output attached below, the PDB file is being read in. For chain A, the number of atoms and the number of residues are correct, as well as the number of incomplete residues ({'truncation_to_alanine': 14}). However, for chain B, the number of incomplete residues ({'truncation_to_alanine': 21}) should be 37. Any ideas? Thanks, Michael **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu **************************************************************** phenix.refine output: Monomer Library directory: "/usr/local/phenix-1.7-650/chem_data/mon_lib" Total number of atoms: 51463 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 6289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6289 <==== matches PDB file Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 14} <==== MATCHES PDB file Link IDs: {'PTRANS': 34, 'TRANS': 746} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan2': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 . . . . Chain: "B" Number of atoms: 6236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6236 <==== DOES NOT MATCH PDB file 780 residues with 6152 atoms Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 21} <==== 37 truncation_to_alanine Link IDs: {'PTRANS': 34, 'TRANS': 745} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved chain link planarities: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLN:plan2': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49

2 1

Detecting and dealing with Pseudotranslation and/or twinning
by Hamaoka, Brent 13 May '11

13 May '11

I’ve been working on a troublesome protein structure. The native protein forms crystals that diffract to 2.75A and belong to P212121 (55.179 64.316 233.748 90.000 90.000 90.000) with 4 molecules in the ASU. I have 3 versions of the same protein where selenomethionine mutations are incorporated at different positions. Interestingly, these mutations cause the protein to form crystals belonging to C2221 (56.130 64.665 240.854 90.000 90.000 90.000). Looking back at the native datasets, Xtraige indicates the largest Patterson peak is (0.5, 0.486, 0), height is 11.8% of the origin peak, and p_value(height) is 0.08549, which is just outside of the threshold for being identified as containing pseudotranslation. Datasets from a couple of the selenomet incorporated crystals yield diffraction to ~3.5A and anomalous signal to ~6.7A. Some of the datasets give a solution with reasonable maps, but the best maps are achieved from combining MAD/SAD selenomet datasets and one from a mercury derivatized crystal using the ‘group’ command in Phenix. --------------------------------------------------------------------------- 5: STEP: finished Top solution: # 39 Dataset #0 BAYES-CC: 69.2 +/- 13.4 FOM: 0.6 Built: 219 Side-chains: 44 Chains: 9 CC: 0.74 Score type: SKEW CORR_RMS NCS_OVERLAP Raw scores: 0.41 0.82 0.00 100x EST OF CC: 69.17 43.34 31.25 --------------------------------------------------------------------------- Maps from this solution show connected electron density that looks like helices, consistent with the predicted secondary structure. Strangely, there is absolutely no side-chain density, only c-beta at most. I can build a poly-ala model into the map and the distances between the heavy atom sites appear correct based upon the known positions of the selenomethionines and the single cysteine in the protein sequence. However the model does not refine. R-free starts and remains near 0.45. I’ve tried indexing in lower symmetry space groups (P2, C2, P1) and re-solving by molecular replacement, but the refinement still fails. Xtriage does not indicate twinning. Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws <I^2>/<I>^2 : 2.305 <F>^2/<F^2> : 0.758 <|E^2-1|> : 0.788 <|L|>, <L^2>: 0.501, 0.333 Multivariate Z score L-test: 1.643 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. One possible clue as to what is going on comes from analysis of SOLVE results. I was analyzing whether SOLVE/PHENIX solutions were related with one another by various origin shifts and came across one particular SOLVE run from a SeMet SAD dataset in C2221 that gave good statistics for a solution FOM=0.57, Z-score=20.26, peak height between 7.1 and 10.8 for 4 SeMet sites to 3.8A). The maps, however, looked poor. What was interesting, though, was that 2 of the Se sites matched well with where I was expecting the Se sites in one molecule in the asymmetric unit. The other two matched with where I would expect the sites in the other molecule when the model is shifted by one half the unit cell distance along the ‘a’ or ‘b’ axis. I’d appreciate any advice as to what might be happening, and how might I go about detecting the problem, and how to dealing with the data? Brent Hamaoka UC San Diego 9500 Gilman Drive 0375 La Jolla, CA 92093

3 2

problem with version 1.7.1-743 linux
by Daniel PANNE 12 May '11

12 May '11

I get the following error only in 1.7.1-743 but not in 1.7_650. Any idea? Thanks, Daniel ******************************************************************************* ERROR: Unused parameter definitions: refinement.main.compute_optimal_errors (file "P1_refine_rigid.eff", line 257) refinement.pdb_interpretation.peptide_link.use_finite_differences (file "P1_refine_rigid.eff", line 514) refinement.secondary_structure.h_bond_restraints.substitute_n_for_h (file "P1_refine_rigid.eff", line 977) refinement.secondary_structure.h_bond_restraints.restrain_initial_values (file "P1_refine_rigid.eff", line 983) refinement.secondary_structure.h_bond_restraints.sigma (file "P1_refine_rigid.eff", line 984) refinement.secondary_structure.h_bond_restraints.slack (file "P1_refine_rigid.eff", line 985) refinement.secondary_structure.h_bond_restraints.h_o_distance_ideal (file "P1_refine_rigid.eff", line 986) refinement.secondary_structure.h_bond_restraints.h_o_distance_max (file "P1_refine_rigid.eff", line 987) refinement.secondary_structure.h_bond_restraints.n_o_distance_ideal (file "P1_refine_rigid.eff", line 988) refinement.secondary_structure.h_bond_restraints.n_o_distance_max (file "P1_refine_rigid.eff", line 989) ******************************************************************************* Sorry: Unused parameter definitions: Please check the input file(s) for spelling errors and obsolete parameter definitions. To disable this error message, add --unused_ok to the command line arguments.

3 2

Technician Position available in Milan
by Sebastiano Pasqualato 12 May '11

12 May '11

Dear all, a technical position is available to work in the Crystallography Unit of the IFOM-IEO-Campus in Milan. (http://www.ifom-ieo-campus.it/joinus/detail_jobs.php?docuID=1566) The position is available immediately, and will be granted until March 2012. We are looking for a person who will be involved in the general management of the Unit's instrumentation, and who will take care of gathering samples from the Unit users, set up crystallization trials and perform biophysical experiments. Hence, we look for a person capable of independently organizing her/his work and with a great attitude to relate with people and work in a team. To apply, please send your CV, together with the name of at least one referee. Informal inquiries are welcome. cheers, Sebastiano PS: sorry for the double posting to those subscribed to both mailing lists. -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

1 0

Multiple pdb entries in phenix.fmodel
by zhangh1＠umbc.edu 12 May '11

12 May '11

Hi, I just wonder for the huge systems which have been split multiple pdb entries, if I provide all the pdb files in a single script of phenix.refine: phenix.fmodel A.pdb B.pdb C.pdb data.mtz whether everything will go correctly? Or I have to merge them into a single pdb and renumber all atoms sequentially? Thanks!

2 1

Re: [phenixbb] mr_rosetta
by Thomas C. Terwilliger 12 May '11

12 May '11

Hi Jermaine, I am sorry for the trouble! I am wondering if rosetta is working quite right? Can you possibly run the regression tests on mr_rosetta: phenix_regression.wizards.test_command_line_rosetta_quick_tests and see if that helps diagnose the problem? All the best, Tom T >> I have been trying a standard run of mr_rosetta and I have stopped at the >> same point (output below). 32 folders were created in the >> GROUP_OF_RESCORE_MR_ROSETTA_1 folder and the mr_rosetta.log files all say >> that saved overall results to a .../results.pkl and the Run log file >> states >> that each job finished. But no further files were written in the Work >> folder >> under each RUN folder and I am assuming there should be a folder with my >> final 20 Rosetta models somewhere. Does this mean there was a failure in a >> subscript? >> ============================================================================== >> >> Starting sub-processes Group of rescore MR rosetta:Rescoring set of >> rosetta >> models... >> ============================================================================== >> >> Splitting work into 32 jobs and running with 4 processors using sh >> background=True in ....MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1 >> >> Starting job 1...Log will be: >> ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log >> Starting job 2...Log will be: >> ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log >> >> thanks, >> JJ >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

2 2

mr_rosetta
by Jermaine Jenkins 11 May '11

11 May '11

I have been trying a standard run of mr_rosetta and I have stopped at the same point (output below). 32 folders were created in the GROUP_OF_RESCORE_MR_ROSETTA_1 folder and the mr_rosetta.log files all say that saved overall results to a .../results.pkl and the Run log file states that each job finished. But no further files were written in the Work folder under each RUN folder and I am assuming there should be a folder with my final 20 Rosetta models somewhere. Does this mean there was a failure in a subscript? ============================================================================== Starting sub-processes Group of rescore MR rosetta:Rescoring set of rosetta models... ============================================================================== Splitting work into 32 jobs and running with 4 processors using sh background=True in ....MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1 Starting job 1...Log will be: ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log Starting job 2...Log will be: ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log thanks, JJ

1 0

Low Resolution Density Modification Problems
by Ian Slaymaker 11 May '11

11 May '11

I am having a problem getting a decent DM map at lower resolutions (8, 10, 12, 20). We have a model for the data (R-factor ~34) at 6.6 A (the model is based on different higher resolution data), and when I try and do DM at anything worse than 6.6, the density no longer covers the model. Any suggestions would be appreciated. Ian Slaymaker USC <http://www-scf.usc.edu/%7Eslaymake/>

2 1

Different R-free values
by Jerome Nwachukwu 10 May '11

10 May '11

Dear all: I find that phenix.refine reports a higher starting R-free than those stated for structures downloaded from the PDB. For instance, the R-free stated in the PDB = 0.287, using Polygon = 0.2880, but the Start R-free from phenix.refine = 0.3114 Is this usual, or is something seriously wrong? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

3 2

error from loop fitting
by Kendall Nettles 10 May '11

10 May '11

I'm trying the loop fitting for the first time and keep getting this error: Reading in sequence probability info and matching to input PDB List of segments read from input PDB file: Segment 0 Start: 225 End: 380 ChainID: 'A' NO MATCH What should be in the sequence file? it is fasta format?it is the entire sequence, or just the loop? I've played with different combinations and keep getting the same error. Best regards, Kendall Nettles

2 1

Diffraction anisotropy
by Ina Lindemann 06 May '11

06 May '11

Hi, I am refining a structure of 2.3A resolution. The R values with and without bulk solvent and anisotropic scale are quite different as you can see here: Start R-work = 0.3751, R-free = 0.5562 (no bulk solvent and anisotropic scale) Final R-work = 0.3741, R-free = 0.5557 (no bulk solvent and anisotropic scale) Start R-work = 0.2298, R-free = 0.2974 Final R-work = 0.2261, R-free = 0.2970 I checked the anisotropy of the data with different tools: Results from Xtriage: Maximum likelihood isotropic Wilson scaling ML estimate of overall B value of None: 39.25 A**2 Estimated -log of scale factor of None: -2.59 Maximum likelihood anisotropic Wilson scaling ML estimate of overall B_cart value of None: 50.10, 0.00, 0.00 50.10, -0.00 25.47 Equivalent representation as U_cif: 0.63, -0.00, -0.00 0.63, 0.00 0.32 Eigen analyses of B-cart: Value Vector Eigenvector 1 : 50.103 ( 0.71, 0.71, -0.00) Eigenvector 2 : 50.103 (-0.71, 0.71, -0.00) Eigenvector 3 : 25.473 (-0.00, 0.00, 1.00) ML estimate of -log of scale factor of None: -2.57 Correcting for anisotropy in the data Results from PHASER: Principal components of anisotropic part of B affecting observed amplitudes: eigenB (A^2) direction cosines (orthogonal coordinates) 8.178 0.9961 0.0879 0.0000 8.178 -0.0879 0.9961 0.0000 -16.357 -0.0000 -0.0000 1.0000 Anisotropic deltaB (i.e. range of principal components): 24.535 Results from Ctruncate: ANISOTROPY CORRECTION (using intensities): Anisotropic scaling (orthogonal coords): | -0.2272 -0.0000 -0.0000 | | -0.0000 -0.2272 0.0000 | | -0.0000 0.0000 0.4543 | Anisotropic U scaling (fractional coords): | -4.451e-05 -5.622e-23 -1.266e-21 | | -5.622e-23 -4.451e-05 -8.929e-22 | | -1.266e-21 -8.929e-22 4.717e-06 | Anisotropic B scaling (fractional coords): | -3.514e-03 -4.439e-21 -9.995e-20 | | -4.439e-21 -3.514e-03 -7.050e-20 | | -9.995e-20 -7.050e-20 3.725e-04 | Eigenvalues: 0.7728 0.7728 1.4543 Eigenvalue ratios: 0.5314 0.5314 1.0000 Resolution limit in weakest direction = 3.156 A Now I am not sure about the severeness of anisotropy and the necessary procedure and would be very pleased if anyone could help. The electron density maps look okay related to the resolution. Has anyone experience with the diffraction anisotropy server or ellipsoidal truncation with data with comparable anisotropy? Thank you for your help in advance Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

2 1

phenix.mr_rosetta error
by Jermaine Jenkins 06 May '11

06 May '11

Hi, I am trying to use phenix.mr_rosetta supplying a local.hhr file and using only the top alignment which is an NMR structure and the pre_refine option. It finishes the mr.model_preparation and writes out two pdbs ( _sculpt and _chain that each have 10 ensembles) but then writes out a empty alignment.ali file (should be 100% identity between the template and the search model). Below is the error I get in the RUN_1.log file. Wrote dummy alignment to /pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali ******************* ERROR ENDING *************** Sorry, the alignment file ['/pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali'] does not have enough lines (6 required, 0 found): Note: last line needs to be '--' ******************* ERROR ENDING *************** Sorry, the alignment file ['../pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali'] does not have enough lines (6 required, 0 found): Note: last line needs to be '--' Thanks, JJ

2 1

Off topic: Apologize for linkedin invitation accident
by Nian Huang 03 May '11

03 May '11

Dear fellows, I am really sorry for the massive invitations from my linkedin account. I was certain that I skipped the sending invitation step from my contact lists and I am not sure how it could still happen in the end. Please delete those emails as you wish and I thank the people who have already added me to the connection. Nian Huang, Ph.D. Dept. of Biochemistry UT Southwestern Medical Center

1 0

Invitation to connect on LinkedIn
by Nian Huang via LinkedIn 03 May '11

03 May '11

LinkedIn ------------Nian Huang requested to add you as a connection on LinkedIn: ------------------------------------------ Felix, I'd like to add you to my professional network on LinkedIn. - Nian Accept invitation from Nian Huang http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/_D6v-a9jXU1vVlzLNqYGbefdvPFwhu… View invitation from Nian Huang http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/_D6v-a9jXU1vVlzLNqYGbefdvPFwhu… ------------------------------------------ Why might connecting with Nian Huang be a good idea? Have a question? Nian Huang's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Nian Huang and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation

1 0

Sulfate ion on 2-fold axis
by J. Fleming 01 May '11

01 May '11

Hi all, I have a sulfate ion sitting on a 2-fold axis of symmetry. If I set all the atom occupancies to 0.5 and refine using phenix.refine (Phenix v. 1.5-2) the occupancies are changed to 0.00 for the sulfur, 1.00 for three of the oxygen's, and 0.72 for the fourth oxygen. Can anyone explain this? Thanks in advance, Jon

4 6

Phenix version 1.7.1 released
by Paul Adams 30 Apr '11

30 Apr '11

The Phenix developers are pleased to announce that version 1.7.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical Interface ------------------- - New interfaces for: phenix.phase_and_build, phenix.mtz2map, phenix.french_wilson - Updates to the Structure comparison GUI, which now allows use of non-identical sequences, and results viewing in PyMol. - A plugin for running multiple sequence alignment Installers ---------- - Graphical installers for Macintosh (installs in /Applications) - Binary installer for 64-bit Mac Intel (OS 10.6 only) New Commands ------------ - phenix.french_wilson (new command): - Implements French & Wilson correction of negative and weak intensities (see Acta Cryst A34:517 [1978]) - outputs modified amplitudes in MTZ format - used internally by default in Phaser GUI and phenix.refine when intensities are provided - phenix.reciprocal_space_arrays (new command): - this tool takes a PDB model and a data file and outputs an MTZ file containing a number of arrays that are typically used in various crystallographic calculations, such as R-factors, maps, refinement targets, etc. The output arrays include: - Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, Hendrickson-Lattman coefficients (input original, computed from model and combined), FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more - phaser.brunett (new command): - automated molecular replacement using incremental exploration, with support for parallelization - quick SSM-superposition-based LLG evaluation for alternative models for the same component - "puzzle"-assembly of solutions for a more complete solution - novel space group determination algorithm that retains possible space groups until they are significantly outperformed by others - handles custom models (used without modification), templates (a PDB template and an alignment, Sculptor is run to create models from it) and homology searches (PDB and alignment obtained from homology search, currently HHPRED and BlastXML; data downloaded from EBI) Structure refinement -------------------- - New output MTZ file that contains original data, amplitudes used in refinement, and map coefficients (this replaces *_map_coeffs.mtz) - French and Wilson procedure automatically applied if intensities are input to refinement - Optional automatic rigid-body grouping by polymer chain (rigid_groups_mode=one_group_per_chain) - Reference model uses a "top-out" restraint potential with a smooth cutoff - Automatic determination of Saenger class for nucleic acid base pairs (if not provided by user) - Ability to run phenix.find_tls_groups internally to obtain atom selections - option: tls.find_automatically=True - Automatic non-bonded distance correction for H-bonded atoms Molecular Replacement --------------------- - phenix.mr_rosetta: - Bug fixes - Added web site with data used in Nature Rosetta+Phenix paper at: http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/ - Added keyword include_solvation_energy=False to allow use of mr_rosetta for membrane proteins. - phenix.automr: - bug fix in residue number input, now allows four-digit IDs Ligands ------- - eLBOW: - Geometries can be generated using CSD Mogul substructure searches of experimental geometries. Estimated standard deviations of the bonds and angles are also included in the restraints file. Visualization ------------- - KiNG (phenix.king): - Improved opening multiple electron density maps: tiered windows, with automatic deciphering of file name to preset sigma levels and colors. - Added -phenix command line option to preset map colors to be more like Coot. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

2 1

TLS group definition
by Andres Palencia 29 Apr '11

29 Apr '11

Dear All, I am trying to refine using TLS parameter as in the attached file generated in ccp4. my protein contains a core part from where are inserted several domains. I am defining each of the insertions as a group and this is fine. The problem comes when I try to define the core protein (discontinuous residue ranges). As example, I want to define residues 1:230, 416:568, 629:794 in chain A of the protein; and in the same group I would like also to include 3 bases of RNA, bases 84-87 of chain B. I have seen several questions related to TLS definitions in the archive mailing list, including an answer from Anastasis Perrakis with files attached which I can not extract, but so far I have not find the solution. Could anybody help on that? thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: palencia(a)embl.fr phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/

2 1

phenix.maps
by Bradley Hintze 28 Apr '11

28 Apr '11

This shows my ignorance about mtz files. I'm having trouble with phenix.find_helices_strands. I got 3kat.mtz from Pavel's database. I run: $ phenix.find_helices_strands 3kat.mtz labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT" and get: PHENIX find_helices_strands Wed Apr 27 13:12:19 2011 Commands: phenix.find_helices_strands 3kat.mtz labin=LABIN FP=2FOFCWT PHIB=PH2FOFCWT # find_helices_strands # # Find secondary structure in a map defined by map coeffs in an input mtz file. # Type phenix.doc for help Input map resolution is 3.1 A Labin line will be: LABIN FP=2FOFCWT PHIB=PH2FOFCWT To change it modify this by specifying FP= and PHIB= [and optionally FOM=] like this: labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT" Map from: TEMP_3kat.mtz using labin LABIN FP=2FOFCWT PHIB=PH2FOFCWT NOTE: ratio_trace_extra increased to 1.3 A as dmin > 3.0 NOTE: rad_sep_trace increased to 0.6 A as dmin > 3.0 Fixing sampling interval rad_sep_trace= 0.6 A Optimizing CA-CA tolerance to obtain ratio of 4.0 for nonamers:atoms Tracing chains at resolution of 3.1 A CCP4: Error in label assignments in LABIN

2 1

Question regarding phenix.fmodel
by zhangh1＠umbc.edu 26 Apr '11

26 Apr '11

Hi, According to the instruction, phenix.fmodel was supposed to calculate Fc only; however, when I try the following 2 scripts, they ended up with different Fc values (at the same hkl point): 1. phenix.fmodel ${PDB} high_resolution=XX 2. phenix.fmodel ${PDB} ${MTZ} The instruction says (2) will output Fcalc that will match the set of Miller indices of the data in reflection_data.mtz file, so I thought 1 and 2 should have the same values at the same hkl points... One more question about fmodel. I have 2 models with different sizes, and want to compare their Fc in the same scale. If I use (1), there will be no scaling by default I think, so the Fc results can be directly compared, right? (A most direct way would be checking the Fc at h0k0l0 point and see whether they are proportional to the molecular size, but it seems phenix.fmodel will ignore this point even I expicitly add it to the MTZ file.) Thanks! Hailiang

2 3

Residue number error after autoMR or PhaserMR
by Zhang yu 23 Apr '11

23 Apr '11

Hi, When I run MR in Phenix, I found that there is a numbering error in the solution PDB file The error is that Phenix numbers residues from 0 again when the residue numbers are over 999, though they belong to the same chain. For example "ATOM 11504 N HIS C 999 -37.389 50.436 57.144 1.00 56.62 N ATOM 11505 CA HIS C 999 -36.908 51.569 57.924 1.00 60.55 C ATOM 11506 C HIS C 999 -37.438 51.479 59.337 1.00 61.73 C ATOM 11507 O HIS C 999 -38.648 51.484 59.549 1.00 60.99 O ATOM 11508 CB HIS C 999 -37.382 52.895 57.326 1.00 63.09 C ATOM 11509 CG HIS C 999 -36.353 53.577 56.478 1.00 66.67 C ATOM 11510 ND1 HIS C 999 -35.280 52.912 55.925 1.00 68.12 N ATOM 11511 CD2 HIS C 999 -36.247 54.865 56.070 1.00 68.95 C ATOM 11512 CE1 HIS C 999 -34.559 53.762 55.214 1.00 69.21 C ATOM 11513 NE2 HIS C 999 -35.122 54.953 55.285 1.00 69.80 N ATOM 11514 N MET C 0 -36.544 51.378 60.309 1.00 64.17 N ATOM 11515 CA MET C 0 -36.992 51.355 61.688 1.00 66.45 C ATOM 11516 C MET C 0 -37.290 52.797 62.083 1.00 68.10 C ATOM 11517 O MET C 0 -37.018 53.716 61.302 1.00 68.58 O ATOM 11518 CB MET C 0 -35.903 50.763 62.605 1.00 67.35 C ATOM 11519 CG MET C 0 -36.051 49.272 62.997 1.00 67.14 C ATOM 11520 SD MET C 0 -36.534 48.947 64.735 1.00 65.84 S ATOM 11521 CE MET C 0 -35.169 49.744 65.675 1.00 66.20 C ATOM 11522 N VAL C 1 -37.840 53.015 63.272 1.00 69.46 N ATOM 11523 CA VAL C 1 -38.160 54.373 63.711 1.00 69.99 C ATOM 11524 C VAL C 1 -36.911 55.251 63.875 1.00 70.28 C ATOM 11525 O VAL C 1 -37.029 56.452 64.122 1.00 70.20 O ATOM 11526 CB VAL C 1 -38.908 54.379 65.057 1.00 70.57 C ATOM 11527 CG1 VAL C 1 -40.322 53.847 64.873 1.00 71.16 C ATOM 11528 CG2 VAL C 1 -38.148 53.537 66.061 1.00 70.54 C" Does anyone has idea about it? Thanks Yu Zhang

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fwd: Workshop on "Soft X-ray Crystallography" at the APS, May 4, 2011
by Nathaniel Echols 23 Apr '11

23 Apr '11

---------- Forwarded message ---------- From: Bi-Cheng Wang <wang(a)bcl1.bmb.uga.edu> To: phenixbb(a)phenix-online.org Date: Fri, 22 Apr 2011 12:13:02 -0400 Subject: Workshop on "Soft X-ray Crystallography" at the APS, May 4, 2011 We would like to call your attention to a workshop associated with the upcoming 2011 APS Users Meeting, which will be held on May 4, 2011 at the APS, Argonne National Laboratory, USA. The title of the workshop is “Soft X-ray Crystallography”. You may find the workshop program at http://2011usersmeeting.conference.anl.gov/APSWK1Agenda.htm The web links for meeting registration and the application for a permit to enter the Argonne National Laboratory are: https://2011usersmeeting.conference.anl.gov/register http://www.aps.anl.gov/Users/Site_Access We hope you will be able to attend the APS Users Meeting and our workshop. All the best, B.C. Wang, John Rose, Gerd Rosenbaum and John Chrzas

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b factors reporting
by Maia Cherney 22 Apr '11

22 Apr '11

To: PHENIX user mailing list<phenixbb(a)phenix-online.org> Date: Thu, 21 Apr 2011 15:09:19 -0600 Subject: Re: [phenixbb] B factor for DNA and Protein Pavel Afonine wrote: > > Yes, this trivial combination of two commands will do it: > > phenix.pdbtools model.pdb keep=protein output.file_name=protein_only.pdb > phenix.pdbtools model.pdb keep=rna output.file_name=rna_only.pdb > phenix.pdbtools model.pdb keep=water output.file_name=water_only.pdb > Dear Pavel, These commands did not work for me (version 1.7-650). I need to report average b factors separately for the protein, water, several ligands and ions, all of them in one chain A. Traceback (most recent call last): File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/pdbtools.py", line 3, in<module> from mmtbx import pdbtools File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/__init__.py", line 3, in<module> import cctbx.array_family.flex File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx/cctbx/array_family/flex.py", line 1, in<module> import scitbx.array_family.flex File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx/scitbx/array_family/flex.py", line 2, in<module> import boost.optional File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/optional.py", line 1, in<module> import boost.python File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 45, in<module> ext = import_ext("boost_python_meta_ext") File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 24, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib/libboost_python.so: undefined symbol: PyUnicodeUCS2_AsWideChar sys.path: /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/iotbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/PyCifRW /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/source/phaser /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/libtbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/share/python /usr/lib/python2.6 /usr/lib/python2.6/plat-linux2 /usr/lib/python2.6/lib-tk /usr/lib/python2.6/lib-old /usr/lib/python2.6/lib-dynload /usr/lib/python2.6/dist-packages /usr/lib/python2.6/dist-packages/Numeric /usr/lib/python2.6/dist-packages/PIL /usr/lib/python2.6/dist-packages/gst-0.10 /var/lib/python-support/python2.6 /usr/lib/python2.6/dist-packages/gtk-2.0 /var/lib/python-support/python2.6/gtk-2.0 /usr/local/lib/python2.6/dist-packages

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Creating cif file of ligands by Elbow/ReadySet
by Ngan Nguyen Bich 22 Apr '11

22 Apr '11

Dear Phenix developers, I'm quite new in crystallography and use PhenixGUI for refinement my protein. I got a problem when I had to create cif file of the new ligand to feed in phenix_refine by Elbow/ReadySet I saw that program creates some bonds shorter or longer compared to the statistic value from the CSD for example. Here are some examples when I play with Elbow (same problem with ReadySet) 1. when I feed program the chemical string, (template PDB file is the mylidand_idea.pdb) CR2 C3 CA3 single 1.569 0.038 and if I choose AM1 optimization CR2 C3 CA3 single 1.602 0.040 2. when I feed program the .pdb file, choose Use geometry for Initial geometry. GYC N CA1 single 1.409 0.020 * GYC N HN1 single 0.902 0.020 GYC N HN2 single 0.901 0.020 GYC SG1 CB1 single 1.797 0.020 GYC SG1 HG1 single 1.204 0.020 GYC CB1 CA1 single 1.500 0.020 GYC CB1 HB11 single 1.006 0.020 GYC CB1 HB12 single 0.972 0.020 GYC CA1 C1 single 1.528 0.020 GYC CA1 HA1 single 1.010 0.020 GYC C1 N2 aromatic 1.412 0.020 GYC C1 N3 aromatic 1.304 0.020 GYC N2 CA2 aromatic 1.505 0.020 ** GYC N3 C2 aromatic 1.349 0.020 GYC N3 CA3 single 1.423 0.020 GYC C2 O2 double 1.370 0.020 GYC C2 CA2 aromatic 1.509 0.020 GYC CA2 CB2 single 1.532 0.020 GYC CA3 C single 1.496 0.020 It's strange to me when comparing * and ** and if I run AM1 GYC CB1 CA1 single 1.533 0.035 GYC CA3 C single 1.564 0.035 as I know, the C-C single bond should be about 1.51. Does anyone get a problem like me? I wonder if I didn't do properly or some thing else, or any suggestion for my case. One more questions is that afterward I found cif file (seemly mmcif file) of my ligand in phenix-1.7-650/chem_data/chemical_components And I'm wondering that How the program use these cif file, or I can use them in which way? Thank you in advance. Best regards, Ngan Nguyen Bich KULeuven Belgium

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