Andreas wrote: > >You can load up a .pdb or .mmcif file and say: > > > >hbonds on; color hbonds yellow > > > >in order to see how the hbonds are being assigned. > > yes, looks nice. > > >It only works for the amino backbone, but I think that it is basically > >correct. > > that's all we need for secondary structure calculations.
OK > >If you could take a look at the hbonds that Jmol is calculating that > would be good. > > Looked at the calculations in AminoPolymer.java, the calculation > of the enery seems to be DSSP-ish. That code is taken from RasMol 2.6b2 (which is in the public domain ... and Jmol has explicit permission from Roger Sayles to use it.) > >Q: What are the patterns that I am looking for to identify sheets? > > browsed up the code to the point to where Helices are calculated and > HBond partner - offsets are stored in mainchainHbondOffsets[]. > > Offsets are required to determine Helices. For sheets it is needed to > store all HBonds in another array. Don't understand what you want to store in that other array ... > Additionally, each amino > acid can be donor or acceptor of two H-bonds. DSSP calls this > "bifurcated" H-bonds. Basically energyMin1, indexMin1 and > energyMin2,indexMin2 in bondAminoHydrogen should be stored and are > needed for method "bond" in the pseudocode below. Are you saying that these values should be stored as entries in this *other* array? > pseudocode to calc sheet H-Bond pattern: > for a in aminos: > for b in aminos: > // testing for parallel : > if ( bond(a+1,b) && bond(b,a-1)) || > ( bond(b+1,a) && bond(a,b-1)) > found parralel bridge > > // testing for antiparallel : > if ( bond(a,b) && bond(b,a)) || > ( bond(a+1,b-1) && bond(b+1,a-1) > found antiparallel bridge. > > and the code for bond: > > boolean bond (i,j) > if ( ( i.acceptor1.index = j && i.acceptor1.energy < cutoff )|| > ( i.acceptor2.index = j && i.acceptor2.energy < cutoff )) > return true ; > else return false, Let me digest this code a bit. > according to the code in AminoPolymer "cutoff" could be -500 which is > also the cutoff used during the calculation of the energy. OK > then we have got the basic elements of sheets: H-Bond bridges. > Several bridges are connected to a sheet if they involve consecutive > residues. > > DSSP allows irregularities -"bulges". This means that on one side of > the sheet a gaps up to 4 residues and on the other side up to 1 > residue are allowed, before the sheet is interrupted. But these > exception rules do not always make sense. Let's discuss these items later. > Hope this helps somehow ... It certainly does. I will try to spend some 'quality time' looking at your pseudocode and get back to you with questions. Miguel ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] ----- ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
