I would like to add that I would appreciate if Jmol would calculate H-bonds between carbohydrate residues, possibly along similar lines to Swiss-pdb viewer.
Richard Steane ----- Original Message ----- From: "Angel Herraez" <[EMAIL PROTECTED]> To: <jmol-users@lists.sourceforge.net> Sent: Tuesday, November 04, 2008 5:05 PM Subject: Re: [Jmol-users] Protein Hydrogen Bonds again > David, a very quick response; I'll need some more time to check > details: > > >> would like Jmol to be able to display H-bonds between amino acid side >> chains and main-chain atoms > > I agree that this would be very interesting, but it seems hard from > the coding side (or we need a volunteer programmer) > > >> Question 1: Jmol will display main- >> chain main-chain H-bonds in proteins read from pdb files in which >> this information (or implied info as secondary structure) does not >> appear to be present. Am I right in thinking that Jmol calculates >> these, presumably while it is calculating secondary structure? > > Bob can tell you more precisely, buit I guess if draws Hbonds based > on atom names (O for carbonyl oxygen, H for peptide amino) and some > simple criterion of distance and/or angle. Not really a stringent > calculation. > > >> Question 2: It was suggested to me that as I have the side-chain H- >> bond info in a relational database (from the HBplus program) I could >> add this to a pdb file, specifying CONECTS, and Jmol would interpret >> this. > > The records are CONECT yes, Jmol would read those and draw solid > covalent bonds, which you don't really want. The way to go is to use > Jmol script "connect" which allows to specify them as Hbonds. > You should set up a script that is run after pdb loading. > >> rather than H-bonding. What I want is to be able to turn this on and >> off in the same way that I can script the current bonds. Anyone shed >> some light on this? > > On and off can be done, but will need the whole list of atoms > involved every time. Well, you can define an atom set and then use a > simple distance filter. > > >> Question 3: If the route suggested in 2 is not really an option, what >> is the team's attitude to adding code to Jmol. A colleague has just >> found some C code a student wrote many years ago that calculates side- >> chain H-bonds. The advantage of this is that we have the source and >> porting from C to Java would be less difficult than porting from some >> other languages (e.g. Fortran). If I proposed it as a 15-week project >> for a Masters student in Computing Science or IT, would this seem >> feasible and would it be welcomed by the team? > > I see that as a wonderful option > Jmol is highly modular, I'm sure that could be easily integrated. > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the > world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
