>>>also, what happens (I haven't tested) if there is an hbond between >>>residue 5A and 8B? >> >> Not sure exactly what you mean here. > > A and B are two chains, so this will be yellow.
Actually, if they are in two chains then they will never be detected. Part of the *good news* was 'backbone hbonds within the same chain' >> If you are concerned that insertion codes might mess things up, then I >> don't think you need to worry ... I believe that Jmol will do the right >> thing. The groupID is not used for this calculation. > > really? What IS used for the calculation? PDB Group sequence numbers cannot be trusted. Insertion codes make that clear. Within each Polymer, Jmol assignes a zero-based sequential groupIndex to each group. This is used for almost everything. PDB chains cannot be trusted either ... they are not really chains of connected atoms. So cleaner Polymer data structures are built within Jmol. >>>it would be colored magenta, if I'm not mistaken, > > I'm pretty sure they would be yellow. Actually, I don't think rasmol > shows inter-chain H bonds. Exactly ... so it is a non-issue for now. >>>but that gives the incorrect impression that these are close to each >>>other in the primary sequence. and what happens when residue numbers >>>are not continuous? >> >> >> Residue numbers are not used at all. >> > > really? How can that be? I'm sure that's what the "offset count" is. > Miguel, how DO you calculate the offsets, then? (Maybe I just don't know > what "GroupIDs" and "Residue numbers" are. I used the terms "GroupIDs" and "Residue numbers" interchangably. The PDB spec probably calls them something like 'residue sequence numbers'. But, there is nothing 'sequential' about them. They can count up, they can count down, they can be negative, they can have gaps. And, they can have a text 'insertion code' to allow them to stick something new between two consecutive integers. So, they are nothing more than unique identifiers. But the value of the identifier says nothing about the sequence within the polymer. >> Q: Is that the desired behavior? > > I think so. This is a pretty minor aspect of the overall display. Really > quite subtle compared to ribbons and such. OK Miguel ------------------------------------------------------- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
