>>- Like RasMol, Jmol only supports backbone hbonds in proteins. On >>the nucleotide side, it only supports those *classical* nucleotide >>hbonds that hold the helix together, whatever they are called. >> > perhaps, under spearate thread or on the rasmol list, someone can > explain to me why this limitation exists. knowing RasMol, I'm sure > there is a good reason - I just don't know it.
My thoughts ... In order to calculate hbonds you need to know the positions of the hydrogens. Most PDB files do not have the hydrogens. To solve the general problem of calculating all hbonds, you need to 'sprout' all the hydrogens ... or at least know where they are. Sprouting the hydrogens is not easy. Remember that we don't have bond orders either. It seems to me that the general case is probably not even solvable. Therefore, the only cases that are calculated are the easy ones. The protein backbone hbond and the *classic* nucleotide ones. If there were other cases which were easily identifiable, then I think that they could be added. 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
