- phenixbb - phenix-online.org

how to fix a secondary structure?
by xinghua qin 17 Jul '10

17 Jul '10

Hi phenixers: Recently I am trying to fix a helice, but found that it is so hard for me because of the poor resolution(3.2A) and also a unvisible loop near it, so is there any way to just fix a helice ? can I get it out of the whole structure to refine it? Best regards Xinghua Qin -- Xinghua Qin College of Biological Sciences No.2, Yuan Ming Yuan West Road Haidian District，Beijing，China，100094 Tel: +86-10-62732672

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How to manually define NCS group for phenix.autobuild?
by J J 15 Jul '10

15 Jul '10

Hello everyone, It is easy to manually define NCS group in phenix.refine, but how to manually define it in phenix.autobuild? phenix.simple_ncs_from_pdb will generate an .ncs_spec file which can be used in autobuild, but what if I want to define ncs group myself, say removing some residues from the automatically detected one. I can manually remove them from the .ncs_spec file, but the operations defined in the .ncs_spec is no longer valid? Thanks in advance Jason U Pitt

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How to define multiple rebuilding region?
by J J 15 Jul '10

15 Jul '10

Dear All, I am trying to use phenix.autobuild to rebuild some poor regions in my model. Since I know which part should be rebuilt, I was thinking using rebuild_chain_list in combination with rebuild_res_end_list and rebuild_res_start_list. The manual suggested: " You can specify more than one region by using the Parameter Group Options button to add lines." What is this Parameter Group Options button? I am running through an .eff file. I have tried something like this: rebuild_chain_list= " 'A, 'B' " rebuild_res_end_list= 50 rebuild_res_start_list=10 However, it does not work. It becomes more obscure to me what if I want to rebuild more than one region in a single chain? Thanks in advance. Jason ------------------------------------------------ University of Pittsburgh School of Medicine 3501 Fifth Avenue Pittsburgh, PA 15261 ------------------------------------------------

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Rwork/Rfree and aniso ADPs
by Roberto Battistutta 15 Jul '10

15 Jul '10

Dear All, I have noticed a (too much?) increment in the difference between Rwork and Rfree upon introduction of anisotropic ADPs, from 18.6/21.6 (isotropic ADPs) to 14.5/20.0. The max resolution is 1.6 A with good statistics. What could be the reason for that? Is 1.6 A too low for anisotropic ADPs in phenix? I would like to keep Rwork/Rfree values nearer, how could I do? 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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Selecting ellipsoid of data
by Frank von Delft 15 Jul '10

15 Jul '10

Hi, is there a tool in phenix that allows me to select an ellipsoid of data -- specified e.g. by the highest resolutions in three reciprocal lattice directions. (Yes, I'm playing with anisotropy, "playing" being the operative word.) phx

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Interpreting new ligands
by Monique Gangloff 13 Jul '10

13 Jul '10

Hi, I have not managed to refine glycans such as beta-L-fucose (FUL) that are not listed in the PHENIX library. I am not sure what the problem is. eLBOW works fine and creates a cif file for FUL. elbow.ligand_linking file.pdb crashes with the following error message: "Fatal problems interpreting PDB file". The refinement works fine when I remove FUL from my pdb file. Any suggestion would be very welcome. Cheers, Monique

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Re: [phenixbb] Occupancy Refinement of substrate and product occupying the same coordinates.
by Joseph Brock 13 Jul '10

13 Jul '10

Hi Ralf and Pavel, Thanks so much for the quick response and advice. I have tried both of your suggestions: To assign different altloc identifiers, with the same res ID, chain ID and different resnames (Ralf) and with the same resname (Pavel). I had thought of this but was afraid it would cause confusion with the associated .cif files. Unfortunately, this appears to be the case. For your strategy Ralf, the .cif and .pdb files created by "phenix.ready_set modified.pdb" and the .cif file created by "phenix.elbow modified.pdb" were all accepted by phenix.refine, however the two molecules were still driven away from each other =( For your strategy Pavel, I could not get phenix.refine to run with either the pehnix.ready_set, or the phenix.elbow outputs. It consistently gives the following .cif file error: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 52 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). I will send to you the appropriate sections of both modified pdb files off list and the associated .cif files. Thanks so much again to both of you for all of your help. Cheers, Joe. _________________________________________________________________ View photos of singles in your area! Looking for a hot date? http://clk.atdmt.com/NMN/go/150855801/direct/01/

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Occupancy Refinement of substrate and product occupying the same coordinates.
by Joseph Brock 13 Jul '10

13 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 13 Jul '10

13 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 05 Jul '10

05 Jul '10

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

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

02 Jul '10

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

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

30 Jun '10

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

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NCS constraints in phenix
by Kenneth Verstraete 30 Jun '10

30 Jun '10

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

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