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 ----- Original Message ----- From: "Egon Willighagen" <[EMAIL PROTECTED]> > > Miguel, > > all the FAH files do not have structure information; no info on residue name, > nor what carbons are the alpha carbons... > > I know you've been looking at secondary structure detection, but what about > alpha carbon detection or even residue detection... I know it might be slow, > but it would be very helpfull to be able to detect certain structure, let's > say alpha carbons to start with... > > I also know that the polyhedral command does a bit of structure detection, > and I was wondering if we could split this out a bit... that is, have a script > command to force detection of certain structures, i.e. alpha carbons, being > a C connected to a N, a C=O... let's just assume we're dealing with proteins > here... that's up to the user of the command (say: find alphacarbon)... > > And when this is in place, we can start add nice graphics to the FAH page... ------------------------------------------------------- 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
