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
