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: 2004-05-14 01:39 Message: Logged In: YES user_id=608250 > a) Sidechains : no. I am looking at someone else's code > right now for hbond finding and it treats each sidechain > differently (it uses Lifson Hagler, as well!). The trick is > knowing which groups are donors, and which are acceptors, > for each of the 20 residues, I think. I'll check. Sounds ugly I do not know what 'Lifson Hagler' means ... I have no chemistry training. > b) Sprouting hydrogens : Sadly, also no idea. I suppose this > is easy enough for backbone amides, as they can be assumed > to be planar. However, hydroxyl groups in sidechains (tyr, ser, > thr) cannot be predicted with any accuracy (I understand) and > the nitrogens in HIS are also difficult. I assume that this is generally the same problem as assigning hbonds. > c) CML Hbonds : sorry, I got you all exicited there! :). I fudged > the markup to have bonds between atoms that I wanted to > have hbonds :( As an aside, I have seen pdb files with hbonds > defined - but I look at a lot of them, so I can't remember which > it was. It isn't very common though. No problem. We just finished implementing the CML reader in Jmol v10, so I was anxious to add enhancements. Thanks for your offer of assistance. If you are interested in helping, I am sure that we can find interesting things that need to be done. Miguel ---------------------------------------------------------------------- Comment By: gilleain maclean torrance (gilleain) Date: 2004-05-14 00:10 Message: Logged In: YES user_id=949974 I forgot to use the scripting window, sorry. a) Sidechains : no. I am looking at someone else's code right now for hbond finding and it treats each sidechain differently (it uses Lifson Hagler, as well!). The trick is knowing which groups are donors, and which are acceptors, for each of the 20 residues, I think. I'll check. b) Sprouting hydrogens : Sadly, also no idea. I suppose this is easy enough for backbone amides, as they can be assumed to be planar. However, hydroxyl groups in sidechains (tyr, ser, thr) cannot be predicted with any accuracy (I understand) and the nitrogens in HIS are also difficult. c) CML Hbonds : sorry, I got you all exicited there! :). I fudged the markup to have bonds between atoms that I wanted to have hbonds :( As an aside, I have seen pdb files with hbonds defined - but I look at a lot of them, so I can't remember which it was. It isn't very common though. So, it looks like I can't be of as much hep as I supposed, sorry about that! gilleain ---------------------------------------------------------------------- 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
