- phenixbb - phenix-online.org

How to use phenix for SAD data
by pramod＠cdfd.org.in 11 Jul '06

11 Jul '06

Hi all i am using the Phenix-GUI first time ,for solving the sad data. I processed my raw data with the mosflm.Further output of the mosflm were used for getting other information or working through this data.so, i started with the strteiges of solve through mad. after setinmg up all the anamolous parameters ,this is always displaying red in the very first in the setup anamolous data gui with the information that format error.i used the format ccp4 unmerged i.e the direct output of the mosflm after integration.i also used the conversion of mtz file into hkl through ccp4 scaling and merging intensities-in which one option i used is the get output as unmerged intensities but, that also didnot worked. suggestions will be appreciated and also i want the deatiled information about how to use the phenix gui properly. with regards Pramod Kumar Junior Research Fellow c/o-Dr.Shekher C Mande Center for DNA Fingerprinting and Diognostics ECIL road Nacharam Hyderabad-76 -

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System requirement
by 崔中利 11 Jul '06

11 Jul '06

Dear all, I am trying to run phenix on a IBM X-31 laptop (1.3G CPU, 256M memory, redhat Fedora Core 3 operation system). But every time it ceased midway. So, can somebody tell me the system requirement to run Phenix? or is any other software required to run Phenix? Zhongli

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Problem on Running Phenix
by 崔中利 07 Jul '06

07 Jul '06

Dear All, I have just installed phenix 1.24.1b and tested my data on this version of Phenix. I tried Autosol. There should be 4 windows to finish the parameter setup according to the documents. But I met a problem after setting the pathway of file of protein sequence (2nd window). The window didn't change to green after I set the pathway and pressed Continue. But from the CPU indicator I knew it was running (100% CPU occupation). And from the log file, I found the program set the resolution automaticlly (3rd window). But after serveral hours' running, I get nothing. What's more, the running sequence was a bit different to the online document of Phenix. The setup window (1st window) appeared first, then the Autosol program window. I don't know what wrong happened to my running, problem of software or my computer. Zhongli

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AUTOBUILD CC
by Noinaj 07 Jul '06

07 Jul '06

Hi, I am new to PHENIX and would like to get a bit of guidance. I am helping a friend with her structure using SAD phasing. She has 4 Se/molecule with 4 mol/ASU. We used Solve to find her sites with nice occupancy, and then ran AUTOBUILD, just to see how it did. It is returning map correlation coeff, Z-scores, etc. What are good numbers for these parameters? Thanks in advance. Cheers, Nick

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Re: [phenixbb] problem when installing phenix 1.24.1b
by Petrus H Zwart 06 Jul '06

06 Jul '06

This most likely means you have downloaded the binairies that do not match your machine architecture. See the readme file: ------------------------------------------------------------------------ ----------- Currently, the following Redhat Linux platforms are tested, and therefore supported for the distribution: - Redhat 8.0 - Redhat 9.0 - Redhat Enterprise Workstation 3 [+/- x86_64] - Redhat Enterprise Server 4.2 [+/- x86_64] - Fedora Core 3 [+/- x86_64] - Fedora Core 5 [+/- x86_64] Redhat versions prior to 8.0 are not supported. PHENIX should also install on other Linux platforms such as Mandrake, or SuSe. There are 4 different Linux installations available, based on the version of the kernel (2.4 or 2.6) and the CPU type (ix86 or x86_64). If it isn't clear which you need then type this command on the machine in question: % uname -rm The first item is the kernel version, the second is the machine hardware. Please download the appropriate installer based on this table: ------------------------------------------------------------------------ - | hardware \ kernel | 2.4 | 2.6 | ------------------------------------------------------------------------ - | ix86 | intel-linux-2.4 | intel-linux-2.6 | ------------------------------------------------------------------------ - | x86_64 | intel-linux-2.4-x86_64| intel-linux-2.6- x86_64| ------------------------------------------------------------------------ - Currently, the following other Unix platforms are tested, and therefore supported for the distribution: - Compaq Tru64 5.1 - SGI Irix 6.5[*] ------------------------------------------------------------------------ ------------ i.e., check if if you have a 2.4 or 2.6 linux kernel and what your cpu type is. for me, I get this: 2.6.11-1.1369_FC4smp i686 i.e, i need the 2.6 , ix86 version. HTH Peter Hi, I met a problem when installing the phenix 1.24.1a. The installer gave me an error information "neither source nor binary availabe, exiting installation". What's wrong with my installation? Zhongli _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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problem when installing phenix 1.24.1b
by 崔中利 06 Jul '06

06 Jul '06

Hi, I met a problem when installing the phenix 1.24.1a. The installer gave me an error information "neither source nor binary availabe, exiting installation". What's wrong with my installation? Zhongli

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run phenix in vitue linux environment
by 崔中利 06 Jul '06

06 Jul '06

I installed phenix 1.1a in a virtue Fedora Core 3 machine with VMware workstation 5 under windows XP on a IBM X31 notebook. When I run autosol (sad) to solve my protein, the system gave me error information "the connection to strategy disrupted" after all parameters are set, but it seems that the program is still running (for the window is still green) . However, the Autosol is showed as Finished in Job control window. Even if I leave the program running overnight, there is no solution produced. Can anyome give me some comments? Zhongli

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PHENIX 1.24.1 beta now available
by Paul Adams 06 Jul '06

06 Jul '06

======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= On behalf of the PHENIX development team I am happy to announce that the next general release version of PHENIX is now available. Binary installers for Linux, SGI and Tru64 platforms are available at our download site: http://phenix-online.org/download/ Current users of PHENIX should upgrade to this most recent release version. To obtain download instructions visit: http://phenix-online.org/phenix_request/ Documentation for PHENIX is available at: http://phenix-online.org/download/documentation/phenix/ There is a PHENIX mailing list at: http://www.phenix-online.org/mailman/listinfo/phenixbb/ There is a PHENIX wiki at: http://www.phenix-online.org/phenix_wiki Please consult the installer README file or online documentation for installation instructions. This is a beta test version, and we therefore look forward to feedback and bug reports from users. Please direct questions and problem reports to: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium: http://www.phenix-online.org/ This version of PHENIX has three main user interfaces: command-line tools, strategies and wizards. Wizards are available under the Wizard tab in the PHENIX GUI, and are designed to complete a complex structure determination process, making automatic decisions when possible, but prompting the user for additional information when necessary. Strategies are available under the Strategy tab in the PHENIX GUI, and are networks of tasks constructed to perform higher-level functions. Version 1.24.1b of PHENIX includes: Wizards (in the PHENIX GUI and from the command-line) ===================================================== - AutoSol - automated structure solution (from processed data to a first map and model) using HySS, SOLVE, RESOLVE, and phenix.refine. - AutoMR - automated molecular replacement, using PHASER. Followed by automated model rebuilding using the AutoBuild wizard. - AutoBuild - automated model building or rebuilding combined with structure refinement, using RESOLVE and phenix.refine. - AutoLig - automated ligand fitting into difference density maps using RESOLVE once a complete protein model is available. Strategies (in the PHENIX GUI) ============================== - Ligand screening against the top 200 ligands in the PDB, using RESOLVE. - Structure solution (MAD/SAD and SIR(AS)/MIR(AS)) combining HySS, SOLVE and RESOLVE. - Phase improvement using maximum likelihood methods in RESOLVE. - Model building using TEXTAL or RESOLVE. Command-line tools ================== - mmtbx.xtriage (comprehensive data quality assessment, including twin analysis) - iotbx.reflection_statistics (analysis of diffraction data) - mmtbx.fest (FA value calculation) - phenix.hyss (anomalous substructure determination) - textal.build (automated model building with TEXTAL) - elbow.builder (generation of ligand coordinates and restraints) - phenix.refine (automated structure refinement) - phenix.geometry_minimization (regularize a structure) - phenix.solve (solve) - phenix.resolve (resolve) - phenix.resolve_pattern (resolve_pattern) - iotbx.mtz.dump (write useful information about a MTZ file) - iotbx.pdb.hierarchy (write useful information about a PDB file) Citing PHENIX ============= If you use PHENIX for solving a structure please cite this publication: PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002). PHENIX Developers ================= Lawrence Berkeley National Laboratory - Paul D. Adams - Pavel Afonine - Ralf W. Grosse-Kunstleve - Nigel W. Moriarty - Nicholas K. Sauter - Peter H. Zwart Los Alamos National Laboratory - Tom C. Terwilliger - Li-Wei Hung - Thiru Radhakannan University of Cambridge - Randy J. Read - Airlie J. McCoy - Laurent C. Storoni Texas A&M University - Jim C. Sacchettini - Tom R. Ioerger - Kresha Gopal - Lalji Kanbi - Erik McKee - Reetal K. Pai - Tod D. Romo - Jacob N. Smith Acknowledgements ================ We are very grateful to the following for making code or libraries available to us: - Alexei Vagin and Garib Murshudov for the CCP4 Monomer Library. - The CCP4 developers for making the MTZ library available to us. - Kevin Cowtan for contributing to the cctbx reciprocal space asymmetric units. - David Abrahams for developing the Boost.Python library. Funding ======= The development of PHENIX is principally funded through the Protein Structure Initiative of the National Institute of General Medical Sciences (NIH) under grant P01GM063210. For further information about the Protein Structure Initiative please visit: http://www.nigms.nih.gov/psi/ We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. For more details please visit: http://www.phenix-online.org/ ======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= -- ========================================================== | Paul Adams, | | Senior Staff Scientist, Physical Biosciences Division | | Head, Berkeley Center for Structural Biology | | Deputy PI, Berkeley Structural Genomics Center | |--------------------------------------------------------| | Building 64, Room 248 | Lawrence Berkeley Laboratory, | | Tel: 510-486-4225 | 1 Cyclotron Road, | | FAX: 510-486-5909 | BLDG 64R0121, | | mailto:[email protected] | Berkeley, CA 94720, USA. | ==========================================================

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New version of Phenix
by 崔中利 05 Jul '06

05 Jul '06

Dear administrator, I have seen the introduction to 1.24.1 beta version of phenix. Why is it still not avalable for download? What is the improvement comparing to version 1.1 alpha? Zhongli

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Problem with remotely displaying PHENIX
by Luca Jovine 01 Jun '06

01 Jun '06

Dear all, While waiting for a Mac OS X version of PHENIX, I have installed it on a Linux server, with the idea of remotely display the GUI on our OS X machines. However, when I try to do so, the GUI briefly opens and then bombs out with the following message: LINUX> phenix Running the PHENIX GUI with /home/xray/luca/bin/phenix/phenix-1.1a/phenix-1.1a/ build/intel-linux/python/bin/python PHENIX distribution located in /home/xray/luca/bin/phenix/ phenix-1.1a/phenix-1.1a/phenix Variable SSH_PATH set to /usr/bin/ssh Variable PYMOL_PATH set to /home/xray/luca/bin/phenix/ phenix-1.1a/phenix-1.1a/pymol Variable RSH_PATH set to /usr/bin/rsh Project Details Project Name: luca Date Stamp : Thu Jun 01 15:56:23 2006 Machine : localhost Directory : /home/xray/luca PDS Server will be on ---------- localhost (localhost) ---------- /home/xray/luca ---------- Port 28537 PID 25355 PDS Server Details User : luca Machine : localhost Directory : /home/xray/luca Port : 28537 PID : 25374 Creating new Data Storage /home/xray/luca/strategies The program 'wxPhenix.py' received an X Window System error. This probably reflects a bug in the program. The error was 'BadWindow (invalid Window parameter)'. (Details: serial 6349 error_code 3 request_code 38 minor_code 0) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) ...has anyone else encountered the same issue, and, if so, managed to solve it? Thanks in advance and best regards, Luca ----------------------------------------------------- Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Center for Structural Biochemistry (CSB) Hälsovägen 7, S-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: luca.jovine(a)biosci.ki.se W3: http://www.biosci.ki.se/groups/ljo/ -----------------------------------------------------

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