On Sunday 06 February 2005 10:08 pm, Miguel wrote: > Nicolas wrote: > > I looked at RasMol Manual and found this : > > > > 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. > > 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.
Correct. What I was asking about was *primairy* structure detection. > 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. Egon ------------------------------------------------------- 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
