Feature Requests item #953260, was opened at 2004-05-13 15:06 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=953260&group_id=23629
Category: Interface Improvements Group: None Status: Open Priority: 5 Submitted By: gilleain maclean torrance (gilleain) Assigned to: Nobody/Anonymous (nobody) Summary: hydrogen bonds Initial Comment: 1) Automatic detection of hydrogen bonds, preferably using energy. 2) Display of these bonds like covalent bonds, yet visibly different. 3) Colouring of the bonds by 'type' (separation between residues). I will be happy to do this... (in fact, I once altered the JmolApplet to show hbonds, read in from cml data). ---------------------------------------------------------------------- >Comment By: Miguel (michaelthoward) Date: 2004-05-13 16:27 Message: Logged In: YES user_id=608250 We could certainly use a little help in this area. Jmol v10 currently has some support for hbonds. They can be read in from .pdb files (although I have never seen a .pdb file that had a hbond defined in it). I did not know that CML had support for hbonds. It would be very easy to add support for this ... the infrastructure is already in place. There is also automatic detection hbonds along the amino acid backbone. It is accessed through the RasMol/Chime command 'hbonds' hbonds are displayed as dotted lines, or as broken cylinders. try the following: load samples/pdb/1crn.pdb hbonds .2 color hbonds lime 'color hbonds type' has not been implemented and needs to be worked on. Q: Do you know of a more general algorithm for detecting hbonds in the sidechains? Q: Do you know of a 'sprout' algorithm which will automatically add the hydrogen atoms? Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=953260&group_id=23629 ------------------------------------------------------- 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
