Nicolas wrote: > Hi, > > I looked at RasMol Manual and found this : > > Structure > > Syntax: structure > The RasMol 'structure' command calculates secondary structure assignments > for the currently loaded protein. If the original PDB file contained > structural assignment records (HELIX, SHEET and TURN) these are discarded. > Initially, the hydrogen bonds of the current molecule are found, if this > hasn't been done already. The secondary structure is then determined using > Kabsch and Sander's DSSP algorithm. Once finished the program reports the > number of helices, strands and turns found. > > > Seems to be what we are looking for.
Nicolas, They are looking for something at a lower level than this. The RasMol documentation above refers to the identification of protein secondary structures from a .pdb file that does not contain structure records for HELIX, SHEET, and TURN. However, it assumes that it is a .pdb file that already has the amino acid residues defined. The structure detection that is needed for FAH is at a level below this. The .xyz files do not have the amino acids identified. Therefore, we would need code which identifies amino acids from individual atoms & their bonds. I am sure that this is an interesting problem and that people have worked on it. It is essentially a pattern match on sub-structures. It seems to me that it is the kind of thing that warrants a literature search prior to starting in on an implementation. It also seems to me that it would be a great project for a graduate student. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
