Phenix on Altix 350 ?
Sir, I would like to install Phenix on an SGI Altix 350 server with five 64 bit intel itanium processors. How do i proceed ? sincerely sankar -- ****************************************************************** Sankar N. Manicka C/o Prof. S. Krishnaswamy Dept. of Genetic engineering School of Biotechnology Madurai Kamaraj University Madurai 625 021 TN INDIA mailto: [email protected] ******************************************************************
I would like to install Phenix on an SGI Altix 350 server with five 64 bit intel itanium processors. How do i proceed ?
As a start, could you try installing the CCI Apps source bundle? It is available here: http://www.phenix-online.org/download/cci_apps/ Installation is very simple: perl cci_apps_python_251_bundle.selfx 5 If this works, it is probably not very difficult to make the full Phenix installer work, too. If the CCI Apps installation doesn't succeed, please send me the full output. Ralf
Hi What are normal values for wxc and wxu during refinement of a twinned structure? I noticed in my log file that these values are large. Thanks Mark
Hi Mark, it's different for each particular target. Also it depends if the normalized or not normalized target is used. In case of twin-refinement the target seems to be not normalized and so the values are "large". The absolute values for wxc and wxu don't tell you much, look rather at Rfree, Rfree-Rwork and the geometry deviations from ideal and decide if it is acceptable at the resolution you do the refinement. Pavel. On 4/15/2008 7:48 AM, Mark Collins wrote:
Hi What are normal values for wxc and wxu during refinement of a twinned structure? I noticed in my log file that these values are large. Thanks Mark _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Sir, I downloaded the cci_apps self extractor from the link. The altix 350 comes with Suse linux so downloaded Suse 9.2 [EM64T] version. The installation failed Running command: ./cci_apps_install_script.csh Build tag: 2008_02_08_1610 Sorry: The installer is not suitable for this platform. Installation aborted. sincerely sankar Ralf W. Grosse-Kunstleve wrote:
I would like to install Phenix on an SGI Altix 350 server with five 64 bit intel itanium processors. How do i proceed ?
As a start, could you try installing the CCI Apps source bundle? It is available here:
http://www.phenix-online.org/download/cci_apps/
Installation is very simple:
perl cci_apps_python_251_bundle.selfx 5
If this works, it is probably not very difficult to make the full Phenix installer work, too. If the CCI Apps installation doesn't succeed, please send me the full output.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- ****************************************************************** Sankar N. Manicka C/o Prof. S. Krishnaswamy Dept. of Genetic engineering School of Biotechnology Madurai Kamaraj University Madurai 625 021 TN INDIA mailto: [email protected] ******************************************************************
Please try again with the *source* bundle as indicated before: cci_apps_python_251_bundle.selfx You'll find this in the middle of the download page: http://www.phenix-online.org/download/cci_apps/ Ralf
Hi I am trying to refine RNA/protein complex with phenix but I have problems with the geometry of the nucleotides Is their any equivalent restraints like "dna-rna_restraints.def" that we find in CNS ? thank you regards Mickael CSB_Aarhus university Denmark
Don't the ccp4 monomer codes Cr, Ur, Gr, Ar code for RNA bases with ideal a-form helicies? i.e. the sugar pucker is restricted, but I'm not sure about the planarity of the bases. On Apr 16, 2008, at 9:56 AM, Ralf W. Grosse-Kunstleve wrote:
Is their any equivalent restraints like "dna-rna_restraints.def" that we find in CNS ?
No, sorry. -- This has come up a few times before. It is on the todo list. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
participants (6)
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Francis E Reyes -
Mark Collins -
mickael blaise -
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Sankar Narayanan Manicka