Forwarded by the list owner.

------ Forwarded Message From: owner-modeller_usage@salilab.org Date: Tue, 18 Mar 2003 19:49:28 -0800 To: modeller_usage-approval@salilab.org Subject: BOUNCE modeller_usage@salilab.org: Non-member submission from ["Tsu-Sheng Wang" tswang@life.nthu.edu.tw]

Dears:

I think you can check MMTSB. There is a program which is caculate RMSD. The web site is http://mmtsb.scripps.edu/doc/rms.pl.html.

Jack ----- Original Message ----- ±H¥óªÌ: "Shiyong Liu" syliu@mdl.ipc.pku.edu.cn œ¬¥óªÌ: "Andrej Sali" sali@salilab.org; "'quentin kaas'" kaas@ligm.igh.cnrs.fr; modeller_usage@salilab.org ¶Ç°e€é´Á: 2003œ~3€ë19€é €W€È 01:10 ¥Dœ®: source code for RMSD programme

Andrej Sali,ÄúºÃ£¡

I want to caculate RMSD between one protein and many other protein structures. I hardly found a good RMSD programme by google. Could you help me give me a RMSD programme?

Shiyong

======= 2003-03-18 07:02:00 ÄúÔÚÀ´‹ÅÖ‹‹´µÀ£º=======

>Possibly so. > >Andrej > >-- >Andrej Sali, Professor >Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and > California Institute for Quantitative Biomedical Research >Mission Bay Genentech Hall >600 16th Street, Suite N472D >University of California, San Francisco >San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) >Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 >Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 >Email sali@salilab.org; Web http://salilab.org > > >> -----Original Message----- >> From: owner-modeller_usage@salilab.org >> [mailto:owner-modeller_usage@salilab.org] On Behalf Of quentin kaas >> Sent: Tuesday, March 18, 2003 7:00 AM >> To: modeller_usage@salilab.org >> Subject: Re: Array too small. Increase MPAIRS >> >> >> I resolved my MPAIRS problem in using the top_heav.lib >> topology library >> instead of the top_allh.lib. As my model is quite big, the >> hydrogens may be >> too numerous to be handled by Modeller. >> Thank you for your help. >> >> Quentin Kaas >> >> Le Lundi 17 Mars 2003 16:08, Andrej Sali a écrit : >> > Without seeing the input/output files, it probably indicates a >> > difficult optimization problem that runs into many overlapping atom >> > pairs. Can you improve the alignment? >> > >> > Andrej >> >> > >.

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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Shiyong Liu ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡syliu@mdl.ipc.pku.edu.cn ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2003-03-19

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