Jan, I think that I worked on the dots code in August 2003 and I do not believe that anyone has ever used it. It may well have bugs/incompatibilities with RasMol/Chime.
> it would be nice if the dots surface consider only the current > selection, e.g. a HEM protein 1mno > http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1mno > restrict protein; > set radius 1.0; # currently not implemented The functionality of controlling the solvent radius is implemented ... but it I implemented the scripting command incorrectly. It works if you say 'set solvent 1.2' ** 10 minutes later ** I just changed this. 'set radius {probe-radius}' and 'set solvent {boolean}' are now two separate commands. Please check it out and see if it works OK for you. Tell me if the behavior is not RasMol/Chime compatible. > set solvent on; > dots on; > # should generate a Connolly surface of the protein part as if alone Q: Do you mean 'alone' as if the other atoms were not in the file? If so, then that is not compatible with RasMol/Chime behavior. Q: Is that what you want? Q: What do other people think? > restrict within(4.2, ligand ); > # cut the surface to show only the binding pocket > select [HEM]; > wireframe 80; > select [O2]; > cpk; > # some nice rendering of the ligand > select protein; > cartoon > # some rendering of the protein part > should generate a nice surface of the HEM and O2 binding pocket of the > protein. I did not understand this part ... Miguel ------------------------------------------------------- This SF.Net email sponsored by Black Hat Briefings & Training. Attend Black Hat Briefings & Training, Las Vegas July 24-29 - digital self defense, top technical experts, no vendor pitches, unmatched networking opportunities. Visit www.blackhat.com _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
