- phenixbb - phenix-online.org

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 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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