- phenixbb - phenix-online.org

constraining alpha-helical geometry in phenix
by Pascal EGEA 05 Jun '08

05 Jun '08

Dear All, I am currently refining a structure at moderate resolution (~3.4A) which is mainly composed of alpha-helices . Is there a way to constrain the backbone geometry of the alpha helical regions in the model used for refinement. Many Thanks, Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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System Administrator Position in Berkeley California
by Paul Adams 04 Jun '08

04 Jun '08

System Administrator 3 Position =============================== The Joint BioEnergy Institute is seeking a Systems Administrator, to be a part of the Technology Division. The scope of this position includes managing scientific computing resources, primarily linux- based clusters and servers, making project and public data accessible in a timely manner to project participants, and integrating the data with existing data from other databases. The Joint BioEnergy Institute (JBEI) is a new multi-organizational research center comprising world-class resources and expertise located in one facility at Emeryville, California. The goal of JBEI is to use rapidly advancing scientific techniques, such as systems and synthetic biology, to accelerate development of the nation's biofuels industry. JBEI is a U.S. Department of Energy funded Bioenergy Research Center, managed by Lawrence Berkeley National Laboratory (LBNL) with partners from 5 internationally recognized scientific institutions: Sandia National Laboratories (SNL), Lawrence Livermore National Laboratory (LLNL), University of California-Davis (UCD), University of California- Berkeley (UCB), and the Carnegie Institution for Science Duties: Plan, organize, prioritize and complete assigned tasks and projects in a timely manner. Frequently and clearly communicate task or project status to customers to either set or negotiate expectations. Under the broad supervision of the Vice President of Technology and the Computational Analysis Director: Provide linux system administration and user support for research groups. This includes system installations, software installations from packages or from source code, distribution upgrades, OS and security patches, system monitoring, disk and file system management, system hardware and peripheral management, backup and recovery management, troubleshooting, and crash recovery. Configure, administer, and troubleshoot various compute clusters, web and database servers, and other services and daemons. Participate in the formulation, planning, organizing, implementation and support of new services or capabilities. Provide basic support for linux desktop systems, including hardware and software installations and upgrades. Support a group of approximately 10 full-time programmers and computational biologists in using JBEI computational resources. Key Success Factors: At least five years linux system administration experience, with responsibility for a wide range of hardware and distributions. Specific areas of required experience include compute cluster and job queuing software administration and support; Apache; Python/Perl; bash/ tcsh, including writing complex Bourne shell scripts; runlevel 1 for critical update or recovery purposes; remote administration, including ssh, remote serial consoles, and remote PDUs; NFS; and monitoring various models of RAID controller. Firm understanding of linux internals including the boot process, kernel versions, and recovery scenarios. Experience with a code management system, preferably CVS or Subversion, as both administrator and code contributor. Experience with relational database operation and maintenance, specifically with MySQL, PostgreSQL or Oracle. Database experience should include database design, implementation, installation, and administration, including backup and restore of large databases. Demonstrated ability to make progress on multiple tasks simultaneously, and to work both independently and as a member of a team. Must be available as needed nights and weekends for critical system updates that cannot be performed during regular lab hours. Application Procedure: This is a full-time one-year Term appointment, renewable under the same conditions, contingent upon the continued availability of funding and work. For consideration apply online at: http://jobs.lbl.gov, select "Search Jobs", and enter job number 21565 in the keyword search field. For more information about JBEI go to: www.jbei.org -- 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. Administrator: Delia Clark [ DNClark(a)lbl.gov ][ 1-510-486-6331 ] --

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optional bits of the CCI Apps installion?
by Ben Eisenbraun 03 Jun '08

03 Jun '08

Hi Phenix Developers, When I install CCI Apps, I end up with a directory that looks like this: $ ls -1 1NSF.pdb cci_apps_build cci_apps_fedora3_py251.selfx cci_apps_install_script.csh cci_apps_sources nsf_d2_peak.sca test_apps Which of the bits are optional and can be deleted without affecting the installation? It seems like the selfx install file is fine to delete. How about the sources directory? $ du -k --max-depth=1 62584 ./cci_apps_sources 125840 ./cci_apps_build 225012 . If the sources directory is not needed, that would save me about 30% of the disk use for the installation, and since I have 2-3 concurrent versions installed, and those versions get pushed around to ~75 machines across the network, every bit I can trim helps. As a side note, I think it might be clearer to refer to the "Opteron" builds of the CCI Apps as AMD64 or x86_64. I didn't see anything on the download page that makes this explicit. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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Group ADP not working
by alebus＠pasteur.edu.uy 03 Jun '08

03 Jun '08

Dear all, I am refining a structure (2.9angs res; P21) with phenix (Version: 1.3b; Release tag: rc6; linux platform) I want to carry on group_ADP refinement, according to the ('lengthy') command line : phenix.refine eden_unique1.hkl hlcoeff_blur.hkl abril28_phenix.pdb input.experimental_phases.labels="PA_BLUR PB_BLUR PC_BLUR PD_BLUR" ordered_solvent=false simulated_annealing=false simulated_annealing.mode=first strategy=rigid_body+individual_sites+group_adp+tls main.ncs=tru e main.number_of_macro_cycles=10 xray_data.low_resolution=15.0 xray_data.high_resolution=2.7 tls_group_selections.params rigid_body_selections.params group_anomalous_1.params elbow.acp_A_pdb.001.cif restraints_edits.params convert_to_isotropic=true everything works just fine (including correct handling of an 'unusual' ligand; selected NCS restraints; TLS; etc)...except for the group ADP : phenix keeps doing individual atom B-factor refinement (e.g. these are some pertinent remarks in the output pdb REMARK ****************** REFINEMENT STATISTICS STEP BY STEP ****************** REMARK leading digit, like 1_, means number of macro-cycle REMARK 0 : statistics at the very beginning when nothing is done yet REMARK 1_bss: bulk solvent correction and/or (anisotropic) scaling REMARK 1_xyz: refinement of coordinates REMARK 1_rbr: rigid body refinement REMARK 1_gbr: group B-factor refinement REMARK ------------------------------------------------------------------------ REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3951 0.4346 -6.345353e+00 -6.295977e+00 REMARK 1_bss: 0.3189 0.3519 -6.182904e+00 -6.132416e+00 REMARK 1_rbr: 0.3199 0.3553 -6.164872e+00 -6.111524e+00 REMARK 1_bss: 0.3197 0.3548 -6.158236e+00 -6.106543e+00 REMARK 1_xyz: 0.3145 0.3612 -6.243414e+00 -6.163029e+00 REMARK 1_adp: 0.2890 0.3327 -6.111496e+00 -6.011406e+00 REMARK 2_bss: 0.2862 0.3290 -6.107396e+00 -6.004629e+00 REMARK 2_xyz: 0.2801 0.3278 -6.104559e+00 -5.995221e+00 REMARK 2_adp: 0.2783 0.3213 -6.062947e+00 -5.954846e+00 REMARK 3_bss: 0.2783 0.3214 -6.063301e+00 -5.955103e+00 REMARK 3_xyz: 0.2755 0.3218 -6.065099e+00 -5.950739e+00 REMARK 3_adp: 0.2751 0.3218 -6.062715e+00 -5.947567e+00 ... and so on, always doing 'X_adp' (and not 'X_gbr') on the different steps... starting from a single value on the B-factor column in the input pdb, of course I end up having individually varied figures in the end, which I don't want I will greatly appreciate any help on what am I doing wrong. Thanks, Alejandro

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phenix.elbow
by Morten Grøftehauge 02 Jun '08

02 Jun '08

Dear Phenix.BB, I wrote a mail earlier about some problems I had with phenix.elbow but it didn't seem to get through. I've solved two of the problems now but also found a new one so I'll try posting again. When you set the --xyz option along with --clean then your .xyz file is deleted. Of course the easy solution is simply to not use --clean but I imagine that it is a minor bug since it doesn't happen with --tripos. Secondly I have a slightly larger problem. When an isoSMILES with more than one molecule is inputted then phenix.elbow joins them up to a single molecule (or places them so closely that all programs, including phenix.elbow, interprets them as one molecule when converting to a format such as mol2 with explicit bonds). For an example try phenix.elbow --output=009_3085017 --write_hydrogens=false --overwrite --clean --tripos --smiles='C=CCN.C1C(O1)CCl' The period is supposed to designate two seperate molecules. Remember to use elbow.become_expert before running that line. I hope someone can help me. Sincerely, -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 52 61 Fax: +45 86 12 31 78 www.bioxray.dk

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shell variable SSH_Path not set
by shivesh kumar 02 Jun '08

02 Jun '08

Dear all, We have installed Phenix in Red Hat Linux enterprises 5. It takes a long time for the GUI to appear with the following message-- Shell variable SSH_Path not set What is the solution of this problem. Thanx in advance for suggestions. shivesh

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Error running cci_apps
by JENDREK 29 May '08

29 May '08

Hi, I've encountered following error running cci_apps (25.05.08 build): Sorry: Error reading CIF file: "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/monomer_library/mod_rnaC2.cif" (IOError: [Errno 2] No such file or directory: '/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/monomer_library/mod_rnaC2.cif') I thought it might be my data fault but the same error appears during test_apps script. I'm running cci_apps on the Mac (Tiger 10.4.11). Funny thing that Phenix 1.3rc2 is running without the problem. I hope someone can help me solve the mystery... Andrzej -- alnyds[at]gmail[dot]com

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prosthetic group
by Bryan W. Lepore 29 May '08

29 May '08

should prosthetic groups be attached to proteins by those LINK or CONNECT records as found in typical PDB files? e-LBOW seems for _ligands_ only. -bryan

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Cyndi Salbego 28 May '08

28 May '08

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Variable energy between 6-18keV, ADSC Q315 Detector, MAD Capable. Focused beam size 20x80micron Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV), ADSC Q315 Detector. Contact csalbego(a)anl.gov for further details. See http://necat.chem.cornell.edu for information on our beamlines and a calendar of available days.

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syntax and alternate conformations
by Mark Collins 28 May '08

28 May '08

Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \ occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }

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