- phenixbb - phenix-online.org

The SASTBX webserver
by Peter Zwart 03 Jun '11

03 Jun '11

Dear All, I would like to advertise our online server featuring some basic SAXS analyses tools. The website http://sastbx.als.lbl.gov/cgi-bin/index.html has functionality for 1. Model intensity calculation (using a Spherical Harmonic Expansion; sastbx.she ) 2. Shape determination (or better: Shape Recovery; sastbx.shapeup) 3. Model alignment (sastbx.zalign) The applications we have developed are build using the SASTBX, an extension of the CCTBX (http://cctbx.sf.net) framework, dedicated to the analyses of SAXS data. The model intensity calculation engine uses an approach similar to CRYSOL and (in our hands) provides model SAXS data of a similar quality as FOXS and CRYSOL. The shape recovery procedure (shapeup) provides an estimate of the shape typically within 1 minute without the need for preprocessing the data (i.e. just feed it your background subtracted SAXS curve and nothing more). You can provide a known model as well for comparison. Some example shape recovery results can be found here: http://sastbx.als.lbl.gov/grant/shapeup/summary.html The examples were prepared utilizing data provided by Edward Snell and coworkers (Grant, T. D., Luft, J. R., Wolfley, J. R., Tsuruta, H., Martel, A., Montelione, G. T. and Snell, E. H. (2011), Small angle X-ray scattering as a complementary tool for high-throughput structural studies. Biopolymers, 95: 517–530). Feel free to contact me or Haiguang Liu (HGLiu(a)lbl.gov) if you encounter any problems or have questions. Regards, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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omit map
by Desi Mail 03 Jun '11

03 Jun '11

Hi everybody, I would like to calculate the omit map around the ligand. I followed the documentation http://www.phenix-online.org/documentation/autobuild.htm#anch159 But the 2Fo density around the ligand is very poor. Any help is appreciated. Thanks Mary Make a SA-omit map around atoms in target.pdb phenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omit Coefficients for the output omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . An additional map coefficients file omit_region.mtz will show you the region that has been omitted. (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz).

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Diamond Light Source phase III beamline proposal - call for support.
by Johan Turkenburg 03 Jun '11

03 Jun '11

Many of you will already have seen the request for Expressions of Interest for the Diamond phase III proposal for "A versatile microfocus beamline with an in-situ side station for macromolecular crystallography at DIAMOND". As one of the co-proposers I would like to urge you to support this proposal and write a letter to this effect. We need as many as possible! Details of the proposal can be found here, with a link where your letter of support can be uploaded: http://www.diamond.ac.uk/Home/Beamlines/PhaseIII/ExpressionsofInterest.html You may already have been contacted by other colleagues in the MX community but this is of high importance to the structural community as a whole, and we especially invite our international colleagues to provide support for this initiative. To help us collate these EOI's and comment on any additional feedback you may have, we would ask you to do this by June 8th. Johan Dr. Johan P. Turkenburg X-ray facilities manager York Structural Biology Laboratory University of York Phone (+) 44 1904 328251 York YO10 5DD UK Fax (+) 44 1904 328266

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elbow question
by wtempel 03 Jun '11

03 Jun '11

Dear colleagues, am I alone in thinking that in my example phenix.elbow gave me more than what I was asking for, specifically atom H11 attached to sulfur? Is it added by elbow, or does it originate from the "--chem=tpp" input? Best regards, Wolfram Tempel command line: phenix.elbow --chem=tpp --mogul phenix version: 1.7.1-743

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GUI for phenix_mr.rosetta
by riya doreen 02 Jun '11

02 Jun '11

Dear phenix developers, Is it possible to run phenix_mr.rosetta from the GUI ? Thanks

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Re: [phenixbb] rosetta_mr autobuild failure - typo fixed
by Thomas C. Terwilliger 02 Jun '11

02 Jun '11

Hi again Joe, Typo below (csh vs bash) fixed in this version of the message. -Tom Hi Joe, I'm sorry for the problems in running mr_rosetta! Getting the set up to work is appearing to be a bit of a challenge, particularly on a mac. So the first problem is this: "dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease Reason: image not found" In the cases that have come up so far, there have been two problems. Here are the solutions to those two problems: 1. The installation of Rosetta cannot be moved after it is compiled. This is because the path to the libraries (as in the error message above) is compiled into Rosetta. So...if you moved this installation around at all, try remaking the installation and keeping it in its original location. 2. In some cases the path to the libraries can be conflicting between PHENIX and some other definition on your system. In this case you can try the following shell command (before running phenix.mr_rosetta): with csh: setenv PHENIX_TRUST_OTHER_ENV 1 or with bash or sh: export PHENIX_TRUST_OTHER_ENV=1 Hopefully...one of those will fix this problem. Now the second problem...I am not sure what the actual error is in this one. The error message you got is not helpful as you say because it refers to a file path on the machine where I created the test. That path does not actually have to exist however (I just ran the test on another machine that is not connected to that directory and it runs fine). This means there is some other problem that is the real one. (I will get rid of this error message so this won't happen in the future). Can you try this: 1. reproduce the problem: phenix_regression.wizards.test_command_line_rosetta_quick_tests \ test_autobuild 2. have a look at the log files: cat run.log # if not empty, may give a big clue more test_autobuild_current.log # look at end of this file for clues 3. the test_autobuild_current.log log file may refer to a sub-process where the actual problem occurs: Log file for autobuilding will be: /Users/terwill/unix/misc/junk/test_autobuild/WORK_1/autobuild.log in this case that autobuild log file, and files in WORK_1/AutoBuild_run_1_/TEMP0 may give additional clues. Let me know what this shows! All the best, Tom T >> >> Hi all, >> >> I wanted to use the rebuilding feature of Rosetta to help improve the R-fators of MR solution in a new space group. I'm using Phenix 1.7.1-743 w/ Rosetta 3.2 on MAC OSX 10.5.8 >> >> installation was succesful, so after editing my .profile to include export PHENIX_ROSETTA_PATH=/usr/local/bin/rosetta, I tried to run the following tests: >> >> 1. phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up >> >> 2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta >> >> 3. phenix_regression.wizards.test_command_line_rosetta_quick_tests >> >> While the first was successful (ALL COMMAND_LINE TEST OK), the second reported the following error: >> >> Error: test_command_line_rosetta failed >> >> Upon subsequently running the test_mr_rosetta.com script created in the subdirectory, the following error was reported: >> >> coords1.ali >> coords1.pdb >> fobs.mtz >> mr_rosetta_quick.eff >> perfect.mtz >> seq.dat >> test3.gz >> test9.gz >> test_mr_rosetta.com >> test_mr_rosetta.log >> Sorry: mr_rosetta failed... >> >> ******************************************************************************** Sorry, a subprocess has failed... >> >> END OF LOG FILE >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log : >> >> SYMMETRY FROM INPUT SOLUTION: CRYST1 25.000 25.000 25.000 90.00 100.00 90.00 P 1 21 1 >> >> Scoring the model >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/coord_mr.1.pdb Relaxing model at 3.0 A, generating and scoring 1 relaxed models >> >> Error message: >> >> child process stderr output: >> command: 'sh >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh' >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh: >> line 3: 11915 Trace/BPT trap >> /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease @relax.flags > relax.log 2>&1 >> Failed to run RELAX >> >> >> ******************* ERROR ENDING *************** >> Failed to run RELAX ...see log file in >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/relax.log >> >> ******************* ERROR ENDING *************** >> >> >> The resulting log file showed the following: >> >> dyld: Library not loaded: >> /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib >> Referenced from: >> /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease >> Reason: image not found >> >> phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following: >> >> Running test_autobuild >> FALED TO RUN: test_autobuild >> ************************************************************** >> Error: test_command_line_rosetta_quick_test failed >> >> After running the resulting test_autobuild.com script, the log file showed: >> >> S_COORD_0001_ed_0005_ed.pdb >> averaged_map_coeffs.mtz >> coords1.pdb >> fobs.mtz >> relax.pkl >> seq.dat >> test_autobuild.com >> test_autobuild.log >> Sorry: Failed to run autobuild >> ERROR MESSAGE: >> Sorry the file >> /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file) >> >> >> The last error message was particularly confusing as that directory indeed does not exist on my machine, put was rather the directory path given as an example in the documentation. >> >> I have two hunches for what could be going wrong, but I unsure how to fix either: >> >> 1. In the phenix documentation it says if using a mac, I might have to download some patches, but I could not find any on the Rosetta dowload page ;(. >> >> 2. The documentation also stipulates to specify a proxy server if behind a firewall using >> export HTTP_PROXY=proxyout.mydomain.edu:8080 >> I am behind a firewall, but on my machine there is no proxy server listed under system prefernces-->advanced-->proxies. I can access my machine using a vpn, but don't know how to tell rosetta to do the same. >> >> Thanks for all your help in advance and sorry that this is so long winded ;) >> >> Cheers, >> >> Joe >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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rosetta_mr autobuild failure
by Joseph Brock 02 Jun '11

02 Jun '11

Hi all, I wanted to use the rebuilding feature of Rosetta to help improve the R-fators of MR solution in a new space group. I'm using Phenix 1.7.1-743 w/ Rosetta 3.2 on MAC OSX 10.5.8 installation was succesful, so after editing my .profile to include export PHENIX_ROSETTA_PATH=/usr/local/bin/rosetta, I tried to run the following tests: 1. phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up 2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta 3. phenix_regression.wizards.test_command_line_rosetta_quick_tests While the first was successful (ALL COMMAND_LINE TEST OK), the second reported the following error: Error: test_command_line_rosetta failed Upon subsequently running the test_mr_rosetta.com script created in the subdirectory, the following error was reported: coords1.ali coords1.pdb fobs.mtz mr_rosetta_quick.eff perfect.mtz seq.dat test3.gz test9.gz test_mr_rosetta.com test_mr_rosetta.log Sorry: mr_rosetta failed... ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log : SYMMETRY FROM INPUT SOLUTION: CRYST1 25.000 25.000 25.000 90.00 100.00 90.00 P 1 21 1 Scoring the model /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/coord_mr.1.pdb Relaxing model at 3.0 A, generating and scoring 1 relaxed models Error message: child process stderr output: command: 'sh /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh' /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh: line 3: 11915 Trace/BPT trap /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease @relax.flags > relax.log 2>&1 Failed to run RELAX ******************* ERROR ENDING *************** Failed to run RELAX ...see log file in /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/relax.log ******************* ERROR ENDING *************** The resulting log file showed the following: dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease Reason: image not found phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following: Running test_autobuild FALED TO RUN: test_autobuild ************************************************************** Error: test_command_line_rosetta_quick_test failed After running the resulting test_autobuild.com script, the log file showed: S_COORD_0001_ed_0005_ed.pdb averaged_map_coeffs.mtz coords1.pdb fobs.mtz relax.pkl seq.dat test_autobuild.com test_autobuild.log Sorry: Failed to run autobuild ERROR MESSAGE: Sorry the file /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file) The last error message was particularly confusing as that directory indeed does not exist on my machine, put was rather the directory path given as an example in the documentation. I have two hunches for what could be going wrong, but I unsure how to fix either: 1. In the phenix documentation it says if using a mac, I might have to download some patches, but I could not find any on the Rosetta dowload page ;(. 2. The documentation also stipulates to specify a proxy server if behind a firewall using export HTTP_PROXY=proxyout.mydomain.edu:8080 I am behind a firewall, but on my machine there is no proxy server listed under system prefernces-->advanced-->proxies. I can access my machine using a vpn, but don't know how to tell rosetta to do the same. Thanks for all your help in advance and sorry that this is so long winded ;) Cheers, Joe

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Setting phenix_env in ubuntu 10 system
by Jobichen Chacko 01 Jun '11

01 Jun '11

Dear All, I recently downloaded and installed phenix 1.7-1-743 on Ubuntu system. I need to run the command " source/usr/local/phenix**/phenix_env.sh" each time to launch the program when running as a command line. If I close that terminal and type the command in a new terminal, it is giving the reply "command not found". How does one set paths so that phenix.refine will be recognized in a new terminal window? I got some suggestiions to edit either ~/.bashrc or ~/.bash_profile and add the appropriate "source" command to it. But when I edit .bashrc phenix is automatically executed when I open a new terminal. I want to run phenix by typing command like "phenix.refine xx.pdb xx.mtz". Please let me know which file I should edit to get this. If possible can any ubuntu user send me a copy of the .bashrc file/or any other required file with environment path for phenix. Thank you for your time. Jobi

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Autobuild Error
by B. Anand 01 Jun '11

01 Jun '11

Dear All, I am using autobuild to rebuild the model after MR. However, it stops with the following error which am I not able to comprehend. Could you please shed some light on this error. Am using phenix version 1.7.1 (Release tag:743). Thanks. With Best Regards, Anand *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_multiple_models: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/RUN_FILE_1.log : utoBuild Run 1 Tue May 31 01:00:15 2011 Build cycle 1 of 16 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 No refinement carried out (may need free R flags) Error message from phenix.refine: 'function' object has no attribute 'as_mtz_dataset' Refinement failed... *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_1_/edited_pdb.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/LAST.LOG may have additional information... 'function' object has no attribute 'as_mtz_dataset' ******************************************************************************** *************ERROR ENDING ******************* ******************************************************************************** *************ERROR ENDING ******************* -- B. Anand, Ph. D. Assistant Professor Department of Biotechnology Indian Institute of Technology Guwahati Guwahati 781039 Assam, India Email: banand(a)iitg.ernet.in anandbasub(a)gmail.com Phone: +91-361-258 2223 Fax: +91-361-258 2249 Web: http://www.iitg.ernet.in/banand/

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Re: [phenixbb] Refining sucrose
by Yuri 01 Jun '11

01 Jun '11

All coot needs to run its real-space refinement is a .cif file as Nigel pointed out. You can also get this file from other ligand library websites (proDrg, hic-cup, etc...). The only catch here is. The name of your sucrose atoms must match, exactly, those in the file. Once you have such file go to the the file drop-down menu and click on Import CIF dictionary in coot. That should enable to rotate the rotatable bonds of your ligand -- Yuri Pompeu

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heavy atoms
by ChenTiantian 01 Jun '11

01 Jun '11

Hi, I am dealing with a complex structure which the ligand contains a atom Iodine, I guess it's because Iodine is heavy atom, the electron density of Iodine turns red after 5 cycles refinement. Anybody coped with similar issue? How to let phenix know that the Iodine atom is part of the ligand? Best, 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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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 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.

1 0

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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