Dear Thao, I don't exactly know what the script "protG_mkpsf.inp" does, but could it be that there are bondlength violations ? I know pymol automatically draws bonds between atoms within a certain range. I myself study nucleic acids, and when I have dihedrals in sugars set wrong Pymol displays the following bond triangle: H / \ C---C Which is not stated in my PSF file, and neither in the PDB file.
My suggestions: check bond restraints (if you override defaults) and bond violations. Hopefully this is of any use. Kind regards, Ramon van der Werf Ph.D. student Radboud University Nijmegen Dept. Biophysical Chemistry Toernooiveld 1 6525 ED Nijmegen The Netherlands > Send Xplor-nih mailing list submissions to > xplor-nih at nmr.cit.nih.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > or, via email, send a message with subject or body 'help' to > xplor-nih-request at nmr.cit.nih.gov > > You can reach the person managing the list at > xplor-nih-owner at nmr.cit.nih.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xplor-nih digest..." > > > Today's Topics: > > 1. Question on "no peptide bond is shown" (Yang, Thao) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 22 Aug 2008 16:30:16 -0500 > From: "Yang, Thao" <YANGT at uwec.edu> > Subject: [Xplor-nih] Question on "no peptide bond is shown" > To: "'xplor-nih at nmr.cit.nih.gov'" <xplor-nih at nmr.cit.nih.gov> > Message-ID: > <E3F0E607B3CF71418CE725F002B5F604418081DC08 at CHERRYPEPSI.uwec.edu> > Content-Type: text/plain; charset="us-ascii" > > I tested run the file "protG_mkpsf.inp" to create the extended structure > of a protein; the output file is "template_protG.pdb." When I display the > extended structure in Rasmol or in Pymol I got the amino acid sequence > with the correct amino acids, but there are not peptide bonds. The > peptide bonds are not formed. I used the default file "protG_mkpsf.inp" > without any modifications. What statement should I change or what is > wrong with this file "protG_mkpsf.inp"? I used "XPLOR-NIH 2.19 version", > run in MAC OS. > > Best regards, > > Thao yang > (Thao Yang, Ph.D. > Associate Professor, Biochemistry > Chem. Dept., UWEC > e-mail: yangt at uwec.edu<mailto:yangt at uwec.edu> > phone: 715 836-4190) > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20080822/5e89a16a/attachment-0001.html > > ------------------------------ > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > > End of Xplor-nih Digest, Vol 66, Issue 5 > **************************************** >
