I asked about representing mainchain-sidechain H-bonds for short three-dimensional hydrogen bonded motifs. Bob replied:
>If the motifs are well-described in the PDB file, this would be no >problem. If they are to be generated from scratch, that's more of a problem. No. The way the thing works is that the H-bonds are generated from the PDB files using HBPlus, which is then parsed by a Perl script to generate a table of H-bonds for the SQL database. The motif definitions are cast as SQL queries to populate the database with them. (They could be done on the fly, but it would be too slow.) When a user makes a query for a particular motif in a particular, the residues are retrieved (as residue numbers), and this info is used to generate a pop-up page with the appropriate PDB file displayed in Jmol and the buttons scripted to to highlight or restrict the display to the motif. Jmol calculates mainchain-mainchain H-bonds on the fly, so if the display is restricted to the motif residues, they show fine, so if Jmol could also calculate the other H-bonds that would be ideal. One alternative would be to query the db for the HBonds associated with the motif and retrieve these, but this would add complexity and might slow things down. The other might appear to be to compute the sidechain-mainchain H-bond for a particular definition. This might be Ok for eg the Asx Turn in which an Asx O at residue 1 is H-bonded to a mainchain NH at residue 3, but for other motifs the mainchain residue can be one of two positions. However Angel suggested: >say, >connect 3.0 (AS?.N??) (SER.O??) hbond >to create Hbonds between nitrogen atoms in Asx and oxygen atoms in >serine if they are less than 3 angstroms apart Which might be more promising, but would require generate pages with different jmol scripts depending on the motif. Sigh. There's probably a good reason why none of the protein graphics programs calculate the mainchain-sidechain H-bonds. David -- _______________________________________________________________ David P.Leader, Biochemistry and Molecular Biology Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader _______________________________________________________________ ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
