- phenixbb - phenix-online.org

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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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

2 1

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

7 11

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/

2 1

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

1 0

"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 |

6 25

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 >

2 1

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

3 2

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

3 2

Re: [phenixbb] is derivative data useful for looking for the missing part of the model?
by Thomas C. Terwilliger 15 Jun '10

15 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 >>

1 0

is derivative data useful for looking for the missing part of the model?
by fn1＠rice.edu 15 Jun '10

15 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

3 4

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 >>

4 3

input sharp phases into phenix.autosol
by Michael Hothorn 14 Jun '10

14 Jun '10

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

1 0

Diffraction Methods GRC, Registration deadline is 27th June
by andrew＠mrc-lmb.cam.ac.uk 12 Jun '10

12 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 27th June, so please apply soon ! ========================================================================= Limited funds are 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: TBA 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: TBA 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: TBC 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

1 0

Job Openings: Industrial Post Doc - Structure Based Drug Design Method R&D
by Lance Westerhoff 11 Jun '10

11 Jun '10

Hello All- Good news! We have the following new position available. We are particularly interested in folks who have experience with xray refinement method research and development, so I figured this list would probably be a good fit. Please contact me if you know of anyone who might be interested: ================= Contact: Dr. Lance M Westerhoff - careers(a)quantumbioinc.com Based at: QuantumBio Inc., 200 Innovation Boulevard, State College, PA 16803 On the Web: http://www.quantumbioinc.com/careers/ Job Purpose: Beginning immediately, QuantumBio Inc, headquartered adjacent to The Pennsylvania State University in State College, PA, is in need of a post doctoral computational Biochemist/Chemist interested in continuing his or her career within a dynamic, small-company environment. Under the direction of Dr. Lance M. Westerhoff, General Manager of QuantumBio, the successful candidate will work with both academic and industrial partners to help transition and validate the novel, quantum mechanically based structure-based drug discovery technologies recently developed in the academic laboratory of Dr. Kenneth M. Merz Jr. to QuantumBios product line. The successful candidate will be integral to this project and will focus his or her efforts on the research and software development aspects necessary to validate and deploy this novel technology across the pharmaceutical industry. The position requires the candidate to have a Ph.D. in Chemistry, Biochemistry, or related field along with experience with the methods and software in the field. Due to the limited number of new work visas available, only American citizens or candidates with valid work permits will be considered at this time. A willingness to publish is required, and experience with C++, high performance programming, or xray refinement methods is a plus. Opportunities for advancement may be available through additional SBIR/STTR-style projects, and industry-supported collaborations. Further, in addition to the research and development duties of the project, the position will afford the successful candidate with access to and experience with QuantumBio's industry partners including a number of pharmaceutical, biotech, and computational firms. To apply, submit cover letter, CV, and one or two representative publications to the Contact above. About QuantumBio: QuantumBio Inc is accelerating drug discovery efforts by providing pharmaceutical, biotechnology companies and life science research organizations with a next generation of Computer-Assisted Drug Design (CADD) and Computer-Assisted Molecular Modeling (CAMM) solutions based on the increased accuracy and power of quantum mechanics. These solutions include a number of options tailored to each customers specific requirements including software licensing, services, and customization. See http://www.quantumbioinc.com/ for more! ================= Thank you for your time! -Lance ____________________ Lance M. Westerhoff, Ph.D. General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

1 0

large coordinate and map shift after simulated annealing
by fn1＠rice.edu 11 Jun '10

11 Jun '10

Hi everyone, I am wondering why large coordinate shift could happen after simulated annealing (no rigid body refinement). Although it helps decreasing R values, it looks like the whole molecule shifts together by about 3 A. Is this normal? I read a post in previous phenixbb, but I still not understand it. Thank you very much! Regards, Fengyun

3 4

Persistant high average B-factor.
by Joseph Brock 10 Jun '10

10 Jun '10

Dear Phenix users, I am currently using version 1.6.1-353 and I'm working on a 1.7A structure that has refined quite well using Individual_sites+individual_adp(isotropic)+occupanices+TLS: Final R-work = 0.1776, R-free = 0.2262 However, I noticed that the average B-factor reported by polygon with these settings was quite high ( < 0.1 of other structures with a similar resolution). Discovering I could not change the value of wxu_scale when using individual_adp+TLS, I went about trying to reduce the average B using the method described here: http://phenix-online.org/pipermail/phenixbb/2007-September/000511.html However, I still can't seem to reduce the average B-factor. I've just done a refinement with the following non-default (extreme) target weight settings: target_weights { wxc_scale = 1.5 fix_wxc = 2 fix_wxu = 0.1 (wxu_scale = 1) But if anything, reducing wxu to such low values makes the avergae B-even higher while concuretnly making the gap between R-values much worse: Final R-work = 0.1602, R-free = 0.2457 This suggests to me that I'm obviously over fitting the data but I'm at a loss on how to proceed. Should i just accept that the automatic scaling used for Phenix TLS wxu is doing a good job and that my structure actually does have an unusually high avergae B? I'm fitting two ligands into density, which is at several places ambiguous, so I would like the most unbiased difference density possible. Many thanks in advance, Joe. _________________________________________________________________ New, Used, Demo, Dealer or Private? Find it at CarPoint.com.au http://clk.atdmt.com/NMN/go/206222968/direct/01/

3 3

Autobuild error message, please help!!!
by 신인철 10 Jun '10

10 Jun '10

Hi, everyone I have a problem in running phenix.automr I started AutoMR with the command: ---------------------------------------------------------------------------- ----- phenix.automr build=True data=ZZZZZZ_H-Nat_x22_P3221_from_P321.sca \ coords='1_SMsp.pdb 2_SMsp.pdb 3_SMsp.pdb 4_SMsp.pdb' \ identity='40 32 29 27' seq_file=ZZZZZZ_seq.dat input_seq_file=ZZZZZZ_seq.dat \ copies=4 ---------------------------------------------------------------------------- ------ AutoMR process seems to be done without any error but during autobuild process, I encounterd an error message as follows ---------------------------------------------------------------------------- ----- Re-using input PDB coordinates in build this cycle Running 3 parallel build jobs Standard build in parallel starting with refine.pdb_1 This is the first try at building this model Setting background=False as nproc=1 Try: 1 building 1 model Try: 2 building 1 model Try: 3 building 1 model Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running 1 at a time with csh in /data1/disk02/icshin/UGI/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0 Starting job 1... **************************************************************************** **** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /data1/disk02/icshin/ZZZ/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0/RUN_FILE_1' icshin_com: No such file or directory. **************************************************************************** **** ---------------------------------------------------------------------------- ---------------------------------------------------------- What am I supposed to do? Please, help me! ------------------------------------------------------- Inchul Shin Structural Biology Lab. CALS. Seoul Nationl Univ.

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how-to change resolve keywords using phenix.multi_crystal_average
by Bjørn Panyella Pedersen 09 Jun '10

09 Jun '10

Dear board I am doing a difficult case of density modification. I get good results using resolve after optimising some keywords. I now want to use multicrystal averaging. This works ok in dmmulti, but I would like to combine it with resolve. For this I have tried phenix.multi_crystal_average, which also runs phenix.resolve, but it uses default keywords for resolve, and I can't find documentation on how to change these keywords. Current maps from phenix.multi_crystal_average are worse that the optimized resolve maps, and I believe this is because of the default resolve settings. Is it possible to control resolve keywords using phenix.multi_crystal_average? And how can I do it? Thanks in advance -Bjørn -- Bjørn Panyella Pedersen, PhD Postdoc PUMPKIN, Centre for Membrane Pumps in Cells and Disease University of Aarhus, Dept. Molecular Biology Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark Phone: +45 89425261 E-mail: bjopp(a)bioxray.au.dk http://www.bioxray.au.dk

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Re: [phenixbb] phenixbb Digest, Vol 55, Issue 7
by ak2197＠columbia.edu 07 Jun '10

07 Jun '10

Ok Alex Sent from my Verizon Wireless BlackBerry -----Original Message----- From: phenixbb-request(a)phenix-online.org Date: Mon, 07 Jun 2010 12:00:01 To: <phenixbb(a)phenix-online.org> Subject: phenixbb Digest, Vol 55, Issue 7 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Robert Ng wants to stay in touch on LinkedIn (Robert Ng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 7 Jun 2010 08:57:29 -0700 (PDT) From: Robert Ng <ubi(a)ufl.edu> To: PHENIX list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Robert Ng wants to stay in touch on LinkedIn Message-ID: <1916754023.4088196.1275926249246.JavaMail.app(a)ech3-cdn13.prod> Content-Type: text/plain; charset="utf-8" LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100607/f95d09c5/a…> ------------------------------ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb End of phenixbb Digest, Vol 55, Issue 7 ***************************************

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Robert Ng wants to stay in touch on LinkedIn
by Robert Ng 07 Jun '10

07 Jun '10

LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation

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A couple of questions regarding twinning
by Pietro Roversi 03 Jun '10

03 Jun '10

Dear all, A couple of questions regarding twinning: 1. The structure I work with has multiple twinning domains (4 to be exact, with pseudo-orthorhombic 222 symmetry induced by twinning in P1). I feed the autobuild script the operators using a keyord: input_files.refine_eff_file_list=mytwinrefinement.eff (see attached file) but only the last one seems to be used. Do I guess correctly that there is only provision for two domains adn therefore the last twinning definition overrides any previously defined one? If so, is there a way of specifying and using multiple twinning domains/operators? 2. Output structure factor amplitudes: are they detwinned? Are they detwinned before the density modification in resolve? and during it? Thanks for any clarification/suggestions Regards Pietro

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Re: [phenixbb] NAG-NAG description
by Chris Ulens 02 Jun '10

02 Jun '10

Thanks for the feedback. I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits. Could you verify my .params file? I get the following error: Empty atom selection refinement .pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122" Thanks. -Chris On 31 May 2010, at 21:34, Georg Mlynek wrote: > Dear Chris, this did it for me. > > > Create a file which you can call whatever you want even the extension > doesn't matter. E.g.: cif_link.params > > Put in this file your links: (Which Atom of residue1 will be > connected to > which Atom in residue2 is already defined in mon_lib_list.cif) > > > > refinement.pdb_interpretation.apply_cif_link { > data_link = NAG-ASN > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname ASN and resid 297 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname NAG and resid 501 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 501 > residue_selection_2 = chain A and resname BMA and resid 502 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = ALPHA1-3. > > residue_selection_1 = chain A and resname BMA and resid 502 > residue_selection_2 = chain A and resname MAN and resid 503 > } > > 4) add this file in the GUI > > > Or run % phenix.refine model.pdb data.hkl cif_link.params > > > 5)Trouble shooting > > a)run iotbx.phil cif_link.params (this checks if the syntax is > right) > > b) check .eff file the links should be added there. You can also > check the . > geo file if you see anything strange. > > c)Having unknown to phenix.refine item in PDB file (novel ligand, > etc... > (BMA is also not there) ). phenix.refine uses the CCP4 Monomer > Library as > the source of stereochemical information for building geometry > restraints > and reporting statistics. If phenix.refine is unable to match an > item in > input PDB file against the Monomer Library it will stop with "Sorry" > message > explaining what to do and listing the problem atoms. If this > happened, it is > necessary to obtain a cif file (parameter file, describing unknown > molecule) > by either making it manually or having eLBOW program to generate it: > > phenix.elbow model.pdb --do-all --output=all_ligands > > this will ask eLBOW to inspect the model_new.pdb file, find all > unknown > items in it and create one cif file for them all_ligands.cif. > Alternatively, > one can specify a three-letters name for the unknown residue: > > phenix.elbow model.pdb --residue=MAN --output=man > > !Check the file if everything is ok! > > > Please correct if this is not ok, or there is an easier way now. > > Kind regards George. > > > -----Ursprüngliche Nachricht----- > Von: phenixbb-bounces(a)phenix-online.org > [mailto:[email protected]] Im Auftrag von Chris Ulens > Gesendet: Monday, May 31, 2010 9:14 PM > An: PHENIX user mailing list > Betreff: Re: [phenixbb] NAG-NAG description > > Dear glycobiologists and phenixfriends. > > I am trying to refine a NAG-NAG chain attached to an Asn122 in my > (pentameric) structure. > What is the proper description in the cif_link.params that is the > equivalent of the pdb description pasted below that phenix so kindly > ignores? > Also, what is the proper way to define the cif_link.params file in the > GUI? > > Thank you. > -Chris > > > LINK ND2 ASN A 122 C1 NAG A 834 1555 > 1555 1.37 > LINK O4 NAG A 834 C1 NAG A 835 1555 > 1555 1.43 > LINK ND2 ASN B 122 C1 NAG B 834 1555 > 1555 1.37 > LINK O4 NAG B 834 C1 NAG B 835 1555 > 1555 1.43 > LINK ND2 ASN C 122 C1 NAG C 834 1555 > 1555 1.37 > LINK O4 NAG C 834 C1 NAG C 835 1555 > 1555 1.43 > LINK ND2 ASN D 122 C1 NAG D 834 1555 > 1555 1.37 > LINK O4 NAG D 834 C1 NAG D 835 1555 > 1555 1.43 > LINK ND2 ASN E 122 C1 NAG E 834 1555 > 1555 1.37 > LINK O4 NAG E 834 C1 NAG E 835 1555 > 1555 1.43 > > --------------------------------------------------- > Chris Ulens, Ph.D. > Lab of Structural Neurobiology > Department of Molecular Cell Biology > Campus Gasthuisberg, ON1 > Herestraat 49, PB 601 > B-3000 Leuven > Belgium > e chris.ulens(a)med.kuleuven.be > t +32 16 345812 > f +32 16 345699 > w http://www.xtal.be > > _______________________________________________ > 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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segmentation fault
by Harry M. Greenblatt 01 Jun '10

01 Jun '10

BS"D Dear All, We had the phenix 1.6.1 GUI running on a fedora core 12 machine; it was thought, for different reasons, that a kernel upgrade would address certain issues unrelated to phenix. The machine is now running 2.6.32.12-115.fc12 (64 bit) and phenix now gives a segmentation fault. Any suggestions? Thanks Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenblatt(a)weizmann.ac.il Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

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Weight optimization
by Jianghai Zhu 28 May '10

28 May '10

Hi, I am using the optimize_wxc=true and optimize_wxu=true in my last refinement. The R and Rfree went down but the RMSDs were way too large. I wonder if phenix.refine still targets the geometry when it optimizes the R and Rfree. Here are the results from almost two identical runs except the weight optimization. 1) optimize_wxc = False optimize_wxu = False wxc_scale=0.08 wxu_scale=1.66 results: R=0.2294 R-free=0.2709 angl=1.087 bond=0.006 2) optimize_wxc = True optimize_wxu = True wxc_scale=0.08 wxu_scale=1.66 results: R=0.2141 R-free=0.2628 angl=2.894 bond=0.033 I am using the dev-412 version. Thanks. -- Jianghai

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offtopic: Problem with Pymol showing maps
by Tatyana Sysoeva 28 May '10

28 May '10

Hi all, if somebody is still not on the memorial day weekend, I have a short question off-topic for Pymol-users I have several maps from Phenix and want to draw some pictures in Pymol. I am opening the files, renamed to ccp4 or map, or not, and all I am getting is just a box, which is not even a unit cell boundary. If you know some nice simple program to do nice pictures of the electron densities- share your knowledge please! Sincerely Tanya

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Super: Rotation and translation
by J. Fleming 28 May '10

28 May '10

Hello, I've been using 'super' to align the c-alphas within one domain of two different models of the same protein while leaving the second domain to move freely. I can do this using: super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca) What I would like to do is determine the rotation and translation of model B's second domain as it moves away from A's second domain. I can output a matrix after running super using: print cmd.get_object_matrix("A") How do I go from the matrix to an angle and distance? Thanks for any thoughts, Jon

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