Hi John, Thanks for your suggestions.
At 11:10 AM 5/23/2006, you wrote: >On May 22, 2006, at 9:06 PM, Mensur Dlakic wrote: > >The ordinary NOE potential energy is not suited to homology-derived >distance restraints, since a large fraction of those are wrong. >A better choice would be to try the Marvin package in xplor, which is >far more error-tolerant. It's designed primarily for automatic >structure determination, and so the examples are geared toward that. >But you can import classic xplor NOEs into Marvin, and you >might have better luck then. > >BTW, where are these homology restraints coming from--Andrej Sali's >package? I've been trying both Modeller-derived distance restraints combined with dihedral and h-bond restraints from Permol ( http://www.biologie.uni-regensburg.de/Biophysik/Kalbitzer/permol/permol.html ) and all Permol-derived restraints. For a single template, Modeller seems to be better. >>Finally, is there a no-hydrogen topology in present version of >>XPLOR that I can use instead of protein.par? > >All of the standard xplor topology files are included in xplor-nih. >Note that you could also just delete the hydrogens from >your PSF with a "delete sele (name h*) end" command. > >--JK Yes, deleting hydrogens would be my preference and this works fine. Thanks. Mensur ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: [email protected] | ==========================================================================
