Hello Charles, Thanks a lot, it now works!
Best regards, Katrine Med venlig hilsen / Best regards Katrine Bugge, PhD Postdoc University of Copenhagen Department of Biology Structural Biology and NMR laboratory (SBiNLab) Ole Maaløes Vej 5 DK-2200 København N [email protected] +45 60134241 -----Original Message----- From: Charles Schwieters [mailto:[email protected]] Sent: 6. oktober 2016 17:26 To: Katrine Østergaard Bugge <[email protected]> Cc: [email protected] Subject: Re: [Xplor-nih] unknown atomic coordinates -error Hello Katrine-- > > I am attempting to calculate a structure of a heterodimer/complex > consisting of a small peptide bound to a protein using Xplor-NIH and > primarily NOE restraints. I am however experiencing some difficulties > in providing a correct psf and/or pdb input (it appears). All of my > attempts end up with an all "unknown atomic coordinates" error > (details below), although the calculation finishes without "irregular > exit" (but with a senseless result). The two proteins are described in a > single psf and pdb file, with segid A and B. > > Here's a little problem: > protocol.initStruct("xComplex.psf") > > protocol.loadPDB("xcomplex.pdb") > As loadPDB auto-generates PSF information, you may be doubling the PSF at this point. Instead, if you need a PSF, use initCoords: protocol.initStruct("xComplex.psf") protocol.initCoords("xcomplex.pdb") If you don't need a PSF (for standard amino acids) simply don't call initStruct: protocol.loadPDB("xcomplex.pdb") Let's see if this helps your calculation... best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
