- phenixbb - phenix-online.org

Occupancy Refinement of substrate and product occupying the same coordinates.
by Joseph Brock 12 Jul '10

12 Jul '10

Dear Phenix community, I have a crystal structure which I believe involves the substrate and product of the enzymatic reaction occupying the same space within the active site. Ideally, I would like to refine their occupancies to sum to a value less than or equal to 1, as one would for alternate conformations of the same molecule. Phenix does not recognize that they both have partial occupancies however, and the steric repulsion consequently drives them apart during refinement. Does anyone have any advice on achieving this? This is a 1.6Å structure using Phenix version 1.6.1-353. Many thanks for all your help in advance, Joe. _________________________________________________________________ Browse profiles for FREE! Meet local singles online. http://clk.atdmt.com/NMN/go/150855801/direct/01/

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Bad selections in phenix.refine
by Mark A Saper 12 Jul '10

12 Jul '10

When running phenix.refine from the GUI, definitions for rigid body groups in phenix.refine that are syntactically wrong, causes the job to just hang with "running" status but no CPU is used. It would be nice if either the GUI checked for valid selections, or if phenix.refine returned an appropriate error code that would be recognized by the GUI. 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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phenix reindex
by Gregor Hagelueken 12 Jul '10

12 Jul '10

Hi, I got the following output from phenix.xtriage: ... The full list of Patterson peaks is: x y z height p-value(height) ( 0.500, 0.500, 0.000 ) : 27.056 (2.355e-03) ( 0.333,-0.488, 0.000 ) : 4.790 (9.454e-01) If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space group operator unit cell of reference setting P 43 (a+b,-a+b,c) x+1/2, y+1/2, z (83.41, 83.41, 42.64, 90.00, 90.00, 90.00) ... I know I can use REINDEX in CCP4 to reindex the data, but is there a way to do it in phenix? Cheers, Gregor

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July 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 12 Jul '10

12 Jul '10

Dear Users, The deadline for Sep/Oct 2010 Collaborative Crystallography proposals will be *July 15, 2010. * ---------------------------------------------------------------------------------------- Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Sep/Oct 2010 allocation period, proposals must be submitted by *July 15, 2010.* The deadline for CC proposals for the time period Nov/Dec 2010 will be Sep 15, 2010. Regards, Banumathi Sankaran

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Run locally/detached
by Roberto Battistutta 12 Jul '10

12 Jul '10

Dear All, what is the exact difference in running a job from the Phenix GUI "locally" or detached"? Is any of the two to prefer (I am working on a Mac Pro, OS X 10.5.8)? Thank you. Bye, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.8275265/67 fax. +39.049.8275239 roberto.battistutta(a)unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923236 fax +39.049.7923250 www.vimm.it

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phenix.maps kick maps: seed and error
by Alastair Fyfe 12 Jul '10

12 Jul '10

Hello, I have started using phenix.maps to calculate some kicked omit maps and had two questions: 1) is there a way to control parameters such as the initial random seed or number of kick iterations? Different runs with the same params and input files appear to give different map coefficient outputs. 2) after what appears to be a successful run on a pdb containing two rna chains and solvent atoms I (a) removed all non-RNA atoms and (b) moved all RNA atoms to corresponding symmetry locations within the ASU. No other changes were involved but I now receive the following python stack trace: Compute maps. Traceback (most recent call last): File "/home/afyfe/phenix/phenix-1. 6.1-357/cctbx_project/mmtbx/command_line/maps.py", line 192, in <module> run(args=sys.argv[1:]) File "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/command_line/maps.py", line 168, in run params = params.maps.map_coefficients) File "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/maps/__init__.py", line 295, in __init__ coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp) File "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/maps/__init__.py", line 257, in map_coefficients_from_fmodel average_maps = False).map_coeffs File "/home/afyfe/phenix/phenix-1.6.1-357/cctbx_project/mmtbx/map_tools.py", line 73, in __init__ map_helper_obj = fmodel.map_calculation_helper() AttributeError: 'twin_model_manager' object has no attribute 'map_calculation_helper' thanks, Alastair

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solve won't run.
by alexander.singer＠utoronto.ca 09 Jul '10

09 Jul '10

Hi -- I installed phenix-installer-1.6-289-intel-linux-2.6.tar on my Fedora Core 5 linux partition and most things run -- but not solve (which I was first trying from autosolve). As recommened by the documentation, when I type phenix.solve, here's what I have --- [root@ausinger oth32_c]# phenix.solve binary=/usr/local/phenix-1.6-289/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=1862380800 /usr/local/phenix-1.6-289/build/intel-linux-2.6/solve_resolve/exe/solve: error w hile loading shared libraries: /usr/local/phenix-1.6-289/build/intel-linux-2.6/l ib/libimf.so: cannot restore segment prot after reloc: Permission denied Do you know what I can do about this? Thanks Alex -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

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Re: [phenixbb] solve won't work
by alexander.singer＠utoronto.ca 08 Jul '10

08 Jul '10

Tom -- what you recommended seemed to work -- phenix.solve doesn't crash out any more, and I'm just trying to see if I get a solution using autosol with my new dataset. Again, thanks and I'll let you know if I find any further problems. Alex -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

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Phenix auto-excluding some reflections
by Sam Stampfer 08 Jul '10

08 Jul '10

Hi, I'm in the process of depositing coordinates for a few structures and I noticed that the "number of unique reflections (observed)" is different in the "refinement statistics section" (108812) (read automatically from the phenix-refined pdb file) versus the "reflections" section (118749). The "cut- off sigma(F)" value is 0.12 (read automatically from the phenix-refined file). What criteria does phenix use to reject these ~10,000 reflections? Thanks! -Sam

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phenix-online.org web server issues on Friday?
by Ben Eisenbraun 06 Jul '10

06 Jul '10

Howdy PHENIXians, One of my users reported a "Error attempting to get current version list: HTTP Error 500: Internal Server Error" on Friday morning last week. Looking through the source, I see: phenix/phenix/utilities/check_version.py which seems to do a version lookup against: http://www.phenix-online.org/download/get_versions.cgi It would be good to set an explicit timeout on the urlopen so the GUI doesn't hang on network errors, web server blow ups, etc. AFAICT, urllib2 uses the default global timeout for the socket module, but socket has no default timeout, so calls to a broken web server can hang your python program. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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TLS refinement in phenix
by Mirage Singh Baliyan 06 Jul '10

06 Jul '10

Dear all, I am refining a 2.25 A structure in phenix using TLS parameters. In the generated PDB there is one ANISOU record along with the ATOM record. I am not understanding this. can anybody help me about this Regards Mirage singh Protein crystallography Laboratory IMTECH (IMTECH is a research establishment of CSIR, india) Chandigarh

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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 04 Jul '10

04 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 01 Jul '10

01 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 25 Jun '10

25 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 22 Jun '10

22 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 21 Jun '10

21 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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