Hi Bryan, You can also access this phenix.refine rigid body refinement through autobuild...you can supply (almost) any phenix.refine commands in a file "refinement_commands.eff" and then say "refine_eff_file=refinement_commands.eff" in autobuild. All the best, Tom On Nov 17, 2010, at 7:55 PM, Pavel Afonine wrote:

Hi Bryan,

you can do rigid body refinement using phenix.refine.

Pavel.

On 11/17/10 5:15 PM, Bryan Lepore wrote:

...

dev-572

my understanding of the autobuild<->refine keyword table on the website is that there's no rigid body available through autobuild - is that right?

-Bryan _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

On Thu, Nov 18, 2010 at 1:17 AM, J. Preben Morth wrote:

I am trying to install phenix on a red hat enterprise 5.5 distribution, but get this following error, when trying to run phenix

...

ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found I do have libstdc++-4.1.2-48.el5 missing excatly the "GLIBCXX 3.4.9' but have ...3.4.8

Which installer did you use? We build multiple versions for 64-bit Linux because of possible binary incompatibilities; usually the one built on FC3 is the most portable. -Nat

Hi Preben We are also running RHEL 5.5, and I have used the fc8 installer. This seems to work fine. Andrew Purkiss-Trew, X-ray Laboratory Manager, Cancer Research UK, London Research Institute. ________________________________________ From: [email protected] [[email protected]] On Behalf Of J. Preben Morth [[email protected]] Sent: 18 November 2010 09:17 To: PHENIX user mailing list Subject: [phenixbb] installation problem Hi phenixbb I am trying to install phenix on a red hat enterprise 5.5 distribution, but get this following error, when trying to run phenix

ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found I do have libstdc++-4.1.2-48.el5 missing excatly the "GLIBCXX 3.4.9' but have ...3.4.8

Is there any one with a helping suggestion best Preben J. Preben Morth, Ph.D Group Leader Membrane Transport Group Nordic EMBL Partnership Centre for Molecular Medicine Norway (NCMM) University of Oslo P.O.Box 1137 Blindern 0318 Oslo, Norway Email: [email protected], [email protected] Tel: +47 2284 0794 http://www.ncmm.uio.no/research/ncmm-embl-group-leaders/ _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.