Bugs item #888841, was opened at 2004-02-01 22:36 Message generated for change (Settings changed) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=888841&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Algorithms Group: None >Status: Closed Resolution: None Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Miguel (migueljmol) Summary: Incorrectly displays connections between atoms Initial Comment: Hi, I have noticed in a number of pdb files that Jmol (which is an absolutely brilliant vis tool... WELL DONE) arbitrarily draws a connecting line between atoms making non- sensicle structures. Initially thought it was because the pdb's were old and had poor format but i have noticed it with new files also. Loaded up the same moleculae in Rasmol and the structure loads fine. So it seems to be something related to the default connect algorithm between atoms that Jmol uses. Here are some of the files/pdbs that this occurs with. None of these anomolies occur in Rasmol 5cpa.pdb - numerous erroneous atomic connections 1e8a.pdb - forms what looks like a spider wec in a beta turn between residues 63-68. 6adh.pdb 5rsa.pdb If you can tell me where in the code i could find the connect algorithm, i'll fix it for you if you like. Thanks, keep up the brilliant work ! Dave Chandler [EMAIL PROTECTED] ---------------------------------------------------------------------- Comment By: Peter Murray-Rust (petermr) Date: 2004-02-02 14:07 Message: Logged In: YES user_id=125666 This is a complex problem and there is no single fix. IMO there are at least three ways of generating connections between atoms: - connect all atoms within bonding distance as generated from covalent radii. This is Jmol's default behaviour. A crude enhancement (don't know whether Jmol uses it) is to have a minimum bonding distance as well - this would suppress some of the junk - take a user-supplied connection table. I am not sure whether Jmol can use this - it would certainly be valuable and I have rraised it before - use atom labels and fragment dictionaries. This is common in proteins and I suspect is what RasMOL does. There are several reasons for getting spider webs, such as disorder, alternate structures, etc. The underlying structure (s) can be very difficult to entangle. Sometimes the bonding is "real" as in boranes and other clusters. If connection tables are not used in Jmol then I suggest this as a priority. To write a protein perception algorithm within Jmol is a lot of work. petermr ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2004-02-01 22:48 Message: Logged In: NO Just checked out the latest code (application is what i'm running) and it has certainly improved on most of the incorrect connections between atoms in 5cpa (still some between hetero atoms) but the errors in 1e8a (wierd spider web in beta turn) and the other two are sitll present, along with most of the other files i've noticed. Cheers Dave Chandler ([EMAIL PROTECTED]) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=888841&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
