- phenixbb - phenix-online.org

Phaser heavy atom sites - question
by Peter Grey 06 Jul '10

06 Jul '10

Dear all, Phaser SAD module found roughly 200 sites of my heavy atom. Phaser writes the location of the sites within an ASU. I am looking for a tool that can transform these sites to the corresponding sites within and just around my model. Thank you in advance for any suggestions, Peter.

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hi
by intekhab alam 06 Jul '10

06 Jul '10

I am a new user to phenix and have just started with Phenix.refine using GUI. I want to fix the co-ordinate of ligand atoms in my structure and then refine it. can anyone help me to do that in phenix GUI. Thanks in advance Regards INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Computational Crystallography Newsletter - Issue 1
by Paul Adams 05 Jul '10

05 Jul '10

Dear Colleagues, I am pleased to announce the publication of the first issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ It features articles, meeting announcements and reports, information on research and other items of interest to crystallographers and users of crystallographic software. The target audience is structural biologists including both students and experts. Anyone interested in publishing articles or other items in the newsletter is encouraged to contact the editor at any time. Submission of text by email using the word-processing templates available online is requested. Cheers, Paul -- 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: Marian Harris [ MSHarris(a)lbl.gov ] [ 1-510-486-6886 ] --

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queueing system support in GUI
by Nathaniel Echols 05 Jul '10

05 Jul '10

The most recent nightly build (dev-457) adds the ability to run jobs on Sun Grid Engine. To activate this feature, go to Preferences->Processes and click "Activate queueing system support"; this will add a queue job option to the menu that appears when you click the Run button. I'm hoping that the default command-line arguments I picked are suitable for most environments. Obviously the filesystem that you run jobs on must be visible both to the host machine and to the machines in the queueing system. The same PHENIX installation must also be accessible from both. You need to be able to submit jobs from the machine that you're running the GUI on. (FYI, you could be running everything on a single multi-core computer - there's no reason why this has to be done on a cluster, but that's what I'm testing it on.) You can view the current queue status from the main GUI via "Show queue status" in the utilities menu. (You can't actually delete jobs from there yet, despite the misleading button that I forgot to remove.) Some caveats: - This should, in theory, run on heterogeneous clusters, but I haven't tried this because all of our systems are 64-bit Linux. - I haven't tried it on Mac either. - There will probably be some weirdness associated with closing the GUI and resuming jobs while still running, especially if you try to abort them. - The built-in parallelization of AutoBuild and the ligand identification program will not play nice with the queueing system when using this mechanism (this is really a defect in queueing systems, not AutoBuild). I think it will be relatively easy to fix this, but for now, you're better off using a single multiprocessor machine for parallel AutoBuild runs in the GUI. - If the queueing system or remote host crashes, the GUI will still think the job is running. Those of you who are interested in using this, please let me know how it works and what features are missing. As always, I fully expect that this will break on some setups. thanks, Nat

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Which is the better way to combine the dataset from different crystals?
by fn1＠rice.edu 02 Jul '10

02 Jul '10

Hi all, I have a question on how to combine two dataset from different crystal of the same protein. The first way I could think of is that, 1) Merge two dataset seperately; 2) Scale them to see whether they are consistent with each other enough as indicated by the R-factor; 3) If the R is low enough, say below 10 or 15%, then take the average for both the F and SIGF. The other way is that, 1) Take the unmerged file from MOSFLM, and reset their batch number; 2) Run SCALA to scale these two unmerged dataset at the same time. Could anyone tell which way is the better or the correct way? Thank you in advance! Alphar

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Reference for phenix.elbow
by Michael Hothorn 30 Jun '10

30 Jun '10

Hi, is there a reference for phenix.elbow? Thanks Michael

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NCS constraints in phenix
by Kenneth Verstraete 30 Jun '10

30 Jun '10

Dear all, I am working on a low resolution dataset (4.2 angstrom) of a multidomain complex. Using MR and density modification with NCS I obtained map in which I am extending/modifying my MR-models for the different domains. I tried to build the mainchain as a polyala model (extending on my MR-models) and then refined my new model in phenix.refine using torsion angle refinement. I have fourfold NCS and I think a this point it would be advantageous to use NCS-constraints instead of restraints. Is this possible in phenix? If I set the coordinate_sigma in de .def file to zero will this result in constrained NCS-refinement? ncs { restraint_group { reference=XXX selection=YYY coordinate_sigma=0.00 b_factor_weight=10 } Thank you very much for your advice, kind regards, Kenneth

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SAD dataset
by sbiswas2＠ncsu.edu 28 Jun '10

28 Jun '10

Hi all, I was trying to run autosol with a sca file. I get the following error message: GUESS FILE TYPE MERGE TYPE sca premerged TARGET LABELS ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU'] Unit cell: (45.947, 88.031, 129.436, 90, 90, 90) Space group: F 2 2 2 (No. 22) CONTENTS: ['AutoSol_run_26_/TEMP0/F222peak_PHX_I_476(+).sca', 'sca', 'premerged', 'F 2 2 2', [45.947000000000003, 88.031000000000006, 129.43600000000001, 90.0, 90.0, 90.0], 2.000299364734313, ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU']] File F222peak_PHX_I_476(+).sca RES: 2.0 Guess of most complete dataset: 1 with resolution of 2.0 for dataset 1 FILE IS: AutoSol_run_26_/LAST.LOG ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked I guess this has something to do with the column label of sca file. How do I fix this? Any help is appreciated. thanks, Shya

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Molecule will not load into coot from Phenix 1.6.2-432
by Subhangi Ghosh 26 Jun '10

26 Jun '10

Hi, I'm using Phenix version 1.6.2-432. When I run phenix.refine, coot opens up, but my molecule does not load. If I open in coot after refinement, molecule still does not load in coot. Please help. Thank you, Subhangi

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NAG clashes: C2 with ND2
by Sam Stampfer 25 Jun '10

25 Jun '10

Hi, I'm in the process of preparing 4 structures for submission to rcsb, and the validation server has pointed out numerous issues with the N-acetyl-glucosamine moieties on my structures. While I have fixed the torsion angles accordingly (using CARP from http://www.glycosciences.de/tools/carp/ as a validation checker) and they stay fixed after phenix refinement, phenix keeps generating 2-2.2 Angstrom clashes between ND2 on asparagine with C2 on the NAG (the linkage is ND2-C1 and the usual distances are at least 2.28 Angstroms). Occasionally, the ND2 to C2 distance is as low as 1.8 Angstroms. This is happening in all my structures and happens independently of the setting of wxc_scale (even for wxc_scale=0.05!) My NAG groups fit the density well, both pre- and post- refinement. Any suggestions? Will rcsb care? These clashes are present in 12 out of 39 NAG moieties. Thanks! -Sam

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PHENIX refine: detached sidechain atoms
by Oliver King 25 Jun '10

25 Jun '10

Hi All, I've noticed that when refining a model in phenix.refine using a PDB file from Refmac, the sidechain atoms of certain residues become detached from the rest of the molecule and appear to float on their own, at least when viewing in Coot. I think this is down to the format of the PDB file. For example the atoms of a Leu residue from a phenix.refine file which displays well is of the form: ATOM 1 N LEU A 8 50.022 -34.247 -5.817 1.00 58.12 N ATOM 2 CA LEU A 8 49.788 -34.905 -4.539 1.00 55.84 C ATOM 3 C LEU A 8 48.339 -35.358 -4.348 1.00 60.39 C ATOM 4 O LEU A 8 48.008 -36.016 -3.360 1.00 68.40 O ATOM 5 CB LEU A 8 50.219 -34.011 -3.373 1.00 57.98 C ATOM 6 CG LEU A 8 51.690 -34.126 -2.975 1.00 65.66 C ATOM 7 CD1 LEU A 8 52.014 -33.170 -1.836 1.00 59.99 C ATOM 8 CD2 LEU A 8 52.020 -35.566 -2.594 1.00 68.57 C where as from a Refmac PDB which also behaves well, it is of the form: ATOM 1 N LEU A 8 50.453 -35.722 -5.617 1.00 20.00 N ATOM 2 CA LEU A 8 49.649 -35.131 -4.482 1.00 20.00 C ATOM 3 CB LEU A 8 50.190 -33.735 -4.147 1.00 20.00 C ATOM 4 CG LEU A 8 51.461 -33.755 -3.275 1.00 20.00 C ATOM 5 CD1 LEU A 8 52.556 -32.768 -3.741 1.00 20.00 C ATOM 6 CD2 LEU A 8 51.082 -33.546 -1.799 1.00 20.00 C ATOM 7 C LEU A 8 48.166 -35.063 -4.824 1.00 20.00 C ATOM 8 O LEU A 8 47.822 -34.257 -5.568 1.00 20.00 O but after refinement in phenix it becomes ATOM 1 N LEU A 8 50.734 -35.936 -5.935 1.00 54.45 N ATOM 2 CA LEU A 8 49.846 -35.185 -4.892 1.00 51.89 C ATOM 3 CB LEU A 8 50.377 -33.761 -4.516 1.00 51.22 C ATOM 4 CG LEU A 8 51.550 -33.730 -3.431 1.00 59.27 C ATOM 5 CD1 LEU A 8 52.457 -32.407 -3.635 1.00 60.88 C ATOM 6 CD2 LEU A 8 51.120 -34.090 -1.879 1.00 55.50 C ATOM 7 C LEU A 8 48.268 -35.042 -5.221 1.00 47.92 C ATOM 8 O LEU A 8 47.989 -34.282 -6.195 1.00 47.32 O and the CD2 atom is now too far away to be part of the residue in Coot Is there an easy way to convert a PDB from Refmac into one which will behave itself when put through phenix.refine? I've tried using phenix.pdb_tools and also putting the model through Molprobity and hoping that that the output would be corrected. Thanks, Olly King

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Defining planarity for Phenix.refine
by Peter Grey 23 Jun '10

23 Jun '10

Dear all, I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ? I am grateful for your advice, Peter

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Re: [phenixbb] AutoMR:Multi-subunit model
by S. Saif Hasan 22 Jun '10

22 Jun '10

Hello, Thanks. When I use the PDB structure with 8 polypeptides as the search model and specify the 8 sequences together, I get this warning from AutoMR- "ASYMMETRIC UNIT TOO FULL (scattering from ensembles =1.82 of total scattering)- TOTAL SCATTERING INCREASED: To get rid of this warning message do one of the following: (1) Increasing the scattering in the ASU (keyword COMPOSITION) because you have more scattering than you thought (2) Decrease the number of ensembles you are packing into the ASU (keywords SOLUTION and SEARCH)" Could this be a problem in missing some additional prosthetic groups ? I did not specify any non-protein groups but the search model has them. -- S. Saif Hasan Graduate Student Department of Biological Sciences Hockmeyer Hall of Structural Biology Purdue University 240 S. Martin Jischke Drive West Lafayette, IN 47907 Quoting "Thomas C. Terwilliger" <terwilliger(a)lanl.gov>: > Hi Saif, > > If I understand you correctly, you can specify the search model with 8 > polypeptides as one PDB file and all 8 sequences (separated by blank lines > or lines starting with ">" in one sequence file. Also component 1 can be > all 8 polypeptides and copies=1. > > All the best, > Tom T > > >> Hello, > >> > >> I have a membrane protein complex made up of 8 different polypeptides > >> present in > >> two copies each (16mer). The asymmetric unit is the octamer, as > determined > >> from > >> previous crystallographic studies. To carry out molecular replacement > with > >> the > >> phases from the published structure in AutoMR, should I specify the > >> coordinates > >> of the search model and its overall sequence identity as one file or > >> should I > >> break it down for each subunit ? Also, for the asymmetric unit contents, > >> should > >> I specify the sequence or mass of each subunit separately (as component > 1, > >> 2 and > >> so on) keeping the number of copies fixed at 1 ? There is no NCS. > >> > >> Thanks. > >> -- > >> S. Saif Hasan > >> > >> Graduate Student > >> Department of Biological Sciences > >> Hockmeyer Hall of Structural Biology > >> Purdue University > >> 240 S. Martin Jischke Drive > >> West Lafayette, IN 47907 > >> > >> > >> > >> > >> > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://phenix-online.org/mailman/listinfo/phenixbb > >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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AutoMR:Multi-subunit model
by S. Saif Hasan 22 Jun '10

22 Jun '10

Hello, I have a membrane protein complex made up of 8 different polypeptides present in two copies each (16mer). The asymmetric unit is the octamer, as determined from previous crystallographic studies. To carry out molecular replacement with the phases from the published structure in AutoMR, should I specify the coordinates of the search model and its overall sequence identity as one file or should I break it down for each subunit ? Also, for the asymmetric unit contents, should I specify the sequence or mass of each subunit separately (as component 1, 2 and so on) keeping the number of copies fixed at 1 ? There is no NCS. Thanks. -- S. Saif Hasan Graduate Student Department of Biological Sciences Hockmeyer Hall of Structural Biology Purdue University 240 S. Martin Jischke Drive West Lafayette, IN 47907

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secondary restraints
by Jianghai Zhu 21 Jun '10

21 Jun '10

Hi, I am using secondary restraints in the phenix.refine. I got the following error message. hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 141:143) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 141:143) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 160:162) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 160:162) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 242:244) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 242:244) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 360:363) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 360:363) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 387:389) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 387:389) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'A' and resseq 455:457) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'A' and resseq 455:457) and (altloc 'A' or altloc ' ') and name O" => 3 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 143:152) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 143:152) and (altloc 'A' or altloc ' ') and name O" => 10 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 156:165) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 156:165) and (altloc 'A' or altloc ' ') and name O" => 10 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 190:193) and (altloc 'A' or altloc ' ') and name H" => 1 donors "(chain 'B' and resseq 190:193) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 222:227) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 222:227) and (altloc 'A' or altloc ' ') and name O" => 6 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 243:251) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 243:251) and (altloc 'A' or altloc ' ') and name O" => 9 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 253:256) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 253:256) and (altloc 'A' or altloc ' ') and name O" => 4 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 278:282) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 278:282) and (altloc 'A' or altloc ' ') and name O" => 5 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 301:305) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 301:305) and (altloc 'A' or altloc ' ') and name O" => 5 acceptors hydrogen_bonds_from_selections: incomplete non-PRO residues in helix. "(chain 'B' and resseq 311:321) and (altloc 'A' or altloc ' ') and name H" => 0 donors "(chain 'B' and resseq 311:321) and (altloc 'A' or altloc ' ') and name O" => 11 acceptors Traceback (most recent call last): File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/refinement/command_line.py", line 71, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/phenix/phenix/refinement/driver.py", line 121, in __init__ h_bond_table = self.sec_str.get_bonds_table(log=log) File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 1023, in get_bonds_table log=log) File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 444, in hydrogen_bonds_from_selections ss_type="helix") File "/nfs/home/jzhu/phenix/phenix-1.6.2-432/cctbx_project/mmtbx/secondary_structure.py", line 652, in _donors_and_acceptors donor_isel.insert(k, n_atoms) IndexError: Index out of range. How do I fix it? Thanks. -- Jianghai

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how to extend R-free set
by Robert Immormino 21 Jun '10

21 Jun '10

Hi, Hopefully I'm just missing something obvious.... I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution. I've tried: phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both. I also tried with phenix.refine phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags" This seems closer, but I get the error: Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement: Thanks, -bob

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find_all_ligands vs. ligand_identification
by Mark A Saper 21 Jun '10

21 Jun '10

Could someone explain the difference between the GUI "ligand_identification" routine and the documented command line "find_all_ligands". The latter appears to have more flexible input parameters. I'm not sure the GUI for ligand_identification is working correctly. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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LAST CHANCE TO REGISTER FOR DIFFRACTION METHODS GRC
by A Leslie 21 Jun '10

21 Jun '10

The biannual Gordon Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine from 18-23rd July. The program covers all aspects of macromolecular structure solution from crystallization to structure solution and refinement and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. The registration deadline is *** THIS COMING SUNDAY, 27th June *** = ======================================================================== Limited funds are still available to support new student and postdoctoral applications, contact andrew(a)mrc-lmb.cam.ac.uk for details. = ======================================================================== Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program Diffraction Methods in Structural Biology, 18-23rd July 2010, Bates College, Lewiston, Maine Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: Bob Sweet 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: Martin Weik 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: Michael Wiener 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. Heterogeneity, low solubility and low resolution: structural pursuit on the ternary Myddosome complex in Toll-like receptor signaling: Hao Wu Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Opportunities fof membrane protein analysis with FELs: Petra Fromme 2. Single particle imaging with pulsed hard Xray lasers: Anton Barty 3. Femtosecond nanocrystallography of membrane proteins using LCSL: John Spence

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"Open in Coot" not working on 1.6.1-357
by Ben Eisenbraun 19 Jun '10

19 Jun '10

Howdy PHENIXians, I can't seem to get the "Open in Coot" option to work in PHENIX. I tested version 1.6.1-357 on 32 and 64-bit linux as well as the OS X Intel version, and while Coot will open, it won't display the working data. 'phenix.find_coot_command' works fine from the command line. On the linux machines, when Coot opens, it doesn't have the "Connected to PHENIX" button. On the OS X Intel machine, it does have the button, but it still won't display the working data. Any ideas? -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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is derivative data useful for looking for the missingpart of the model?
by Jacob Keller 16 Jun '10

16 Jun '10

> Hi Fengyun, > > How have you determined whether you in fact have the full-length protein > in your crystals? It sounds like, from your statistics, that everything is > already modelled--it seems hard to believe that 80% of the whole protein > would give such good R values. Do others agree? > > You could run some of your crystals on a gel next to a sample which is > known to be full-length, and you could get the answer. > > Jacob > > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: j-keller2(a)northwestern.edu > ******************************************* > > ----- Original Message ----- > From: <fn1(a)rice.edu> > To: <phenixbb(a)phenix-online.org> > Sent: Tuesday, June 15, 2010 5:59 PM > Subject: [phenixbb] is derivative data useful for looking for the > missingpart of the model? > > >> Hi everyone, >> >> I got a partial model, consisting of 80% of the whole molecule, from the >> molecular replacement. The native data reflects to 2.3 A, and now the >> R/Rfree= 0.22/0.28. My problem is that the missing part of the model is >> important for us, but there is not any density for this region now. >> >> Meantime, we have several heavy atom derivative data. My question is >> that if refine the model against the derivative data, will the heavy >> atom appear in the difference map if existing? Any suggestions on how to >> use the derivative data to locate the missing part of model? >> >> Thanks in advance! >> Regards, >> Fengyun >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >

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phaser spacegroup within phenix
by John M. Berrisford 16 Jun '10

16 Jun '10

Hello I've just spotted a discrepancy between phenix run from ccp4i and from the phenix GUI regarding spacegroup selection run phaser runs. Within the CCP4 GUI you can specify the space group for a phaser molecular replacement run to be the space group of the mtz or a sub-space group (i.e P222 or P212121 etc...). For some reason this isn't as obvious within the phenix GUI. I have an mtz processed in P21 and when I load it into the phenix phaser GUI it tells me its P21 (P 1 21 1) and gives me no other options. However, when I run the molecular replacement job it decides that the space group could be either P2 or P21 and runs both - which in my case runs in P2 and gives a partial solution, not the full solution I would expect in P21. A bit annoying as I know my space group is actually P21. After a few minutes of head scratching, the only way I found to fix it to run in P21 is to enter the "other settings" menu and select "none" within "alternative space groups". I guess this is what your suppose to do, but its not obvious. Can the phenix GUI be changed so that its as obvious as the ccp4 GUI as to what is actually going to run when you press "run". Thanks John I'm running phenix 1.6.1 on OS X. -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44 1223 252882

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Re: [phenixbb] phaser spacegroup within phenix
by John M. Berrisford 16 Jun '10

16 Jun '10

Hi Nat I don't think its a bug, just phaser getting a little bit confused. Phaser ran in both P2 and P21 using the phenix default, not P21 - the space group of the mtz. This default is probably the right thing to do if you don't know the space group of your crystal, but then you wouldn't have scaled the mtz in P21. In my case the reason phaser failed to find a solution is that the P2 solution had a higher initial LLG than the P21 solution while finding the first copy of 4 in my A.U.. So phaser picked P2 to continue the molecular replacement and subsequently stopped due to clashes during packing. John On Tue, Jun 15, 2010 at 8:45 AM, John M. Berrisford <jmb(a)mrc-mbu.cam.ac.uk>wrote: > > I have an mtz processed in P21 and when I load it into the phenix phaser > > GUI it tells me its P21 (P 1 21 1) and gives me no other options. However, > > when I run the molecular replacement job it decides that the space group > > could be either P2 or P21 and runs both - which in my case runs in P2 and > > gives a partial solution, not the full solution I would expect in P21. A bit > > annoying as I know my space group is actually P21. > > After a few minutes of head scratching, the only way I found to fix it to > > run in P21 is to enter the "other settings" menu and select "none" within > > "alternative space groups". I guess this is what your suppose to do, but its > > not obvious. > Point taken - I'll move this to the main window (and label it more clearly - sorry). The result you're describing sounds like it might be a bug, though; shouldn't Phaser try P21 as well and get the full solution, instead of settling for P2? This is what I would expect for the default behavior. -Nat -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44 1223 252882

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Re: [phenixbb] is derivative data useful for looking for the missing part of the model?
by Thomas C. Terwilliger 16 Jun '10

16 Jun '10

Hi Francis, Yes, you can do that. It requires one extra step to do the combination. You need to make a script like the one below (see https://solve.lanl.gov/Resolve/html_resolve_manual/resolve_sample_scripts.h…): All the best, Tom T Merging phase sets with different origins You can merge phase sets with different origins with this script. It uses an FFT convolution to find the best allowed offset between the maps calculated with the two phase sets. Merging the files REQUIRES HL coefficients (see above for generating them if you do not have them). Note: the FP and SIGFP in the output file will come from the hklin file NOT the hklmerge file: phenix.resolve <<EOD hklin random_1_hl.mtz ! File with target map (fixed) labin FP=FP PHIB=PHIM FOM=FOMM HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM hklmerge random_2_hl.mtz ! File to be offset labmerge FP=FP PHIB=PHIM FOM=FOMM HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM hkl_offset_file resolve_off.mtz ! The hklmerge file, offset all by itself hkl_merge_file resolve_merge.mtz ! The hklmerge file offset, then merged with hklin EOD >> Thanks so much!It looks promising. >> If I have two or more derivative data and want to combine all these >> information. Can I just do MRSAD individually for each dataset, and >> combine them? >> >> >> ÒýÓÃ Nathaniel Echols <nechols(a)lbl.gov>£º >> >>> On Tue, Jun 15, 2010 at 4:03 PM, Francis E Reyes >>> <Francis.Reyes(a)colorado.edu >>>> wrote: >>> >>>> Using the model to find the heavy atom sites and then calculating >>>> phases on >>>> those sites (without model) might help. ( I believe phenix will output >>>> a >>>> phase combined map (model + experimental phases)). >>>> >>> >>> Correct, this is the default behavior if you provide a model directly to >>> AutoSol (or Phaser). There is however a semi-automatic way to use the >>> model >>> phases to find sites without biasing the experimental map; see the >>> documentation here: >>> >>> https://www.phenix-online.org/version_docs/1.6.2-432/autosol.htm#anch126 >>> >>> (The AutoBuild step is optional - you could just look at the >>> density-modified map after AutoSol is done.) >>> >>> -Nat >>> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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is derivative data useful for looking for the missing part of the model?
by fn1＠rice.edu 16 Jun '10

16 Jun '10

Hi everyone, I got a partial model, consisting of 80% of the whole molecule, from the molecular replacement. The native data reflects to 2.3 A, and now the R/Rfree= 0.22/0.28. My problem is that the missing part of the model is important for us, but there is not any density for this region now. Meantime, we have several heavy atom derivative data. My question is that if refine the model against the derivative data, will the heavy atom appear in the difference map if existing? Any suggestions on how to use the derivative data to locate the missing part of model? Thanks in advance! Regards, Fengyun

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Re: [phenixbb] input sharp phases into phenix.autosol
by Thomas C. Terwilliger 15 Jun '10

15 Jun '10

Hi Michael, If I understand correctly, you want to take a file that has experimental phases, density modify it, and autobuild a model. Plus you want to take the inverse hand of the phases and do the same thing. For the first part you have two easy options: phenix.autobuild my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file phenix.build_model my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file These do more or less the same thing, but build_model is a lot faster (but not quite as good), and requires version 1.6.2-242 or higher. For phases from sharp, you will want to specify the columns of data to be used for FP SIGFP PHIB FOM HLA HLB HLC HLD for each method above. (The way to specify these are different in the two methods. For autobuild you just list the column labels to be used for the above items with labels="myFP mySIGFP myPHIB myFOM myHLA myHLB myHLC myHLD", and for build_model you specify a regular labin line: labin="FP=myFP SIGFP=mySIGFP...etc" For the second part, flipping the hand of a file with experimental phases...I am not sure if we have a tool for that. Perhaps someone else can comment. All best, Tom T >> Hi, >> >> I hope what I want to do is not considered a crime :-) Is there a way to >> input phases e.i. from sharp into phenix.autosol (preferably the command >> line version) to run resolve with both hands and autobuild for a SAD or >> SIRAS case? >> >> Thanks! >> Michael >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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