From: Frieda R. <fr...@ns...> - 2006-10-04 14:51:44
|
Long delayed response on this thread... Frieda wrote: > I am getting only very > partial surfaces on e.g., 1mbo.pdb (myoglobin) and on other pdb files > as well. Is there something more to it than just opening the file, > selecting protein, and issuing the command? Bob Hanson wrote: > The problem is those water molecules. Yes, we need a new > option. This is to ignore a certain set of atoms, in this case the > water > molecules. Here you go, just uploaded: > > isosurface ignore(solvent) sasurface > > This tells Jmol you don't want the surface around the water molecules. OK, I have now tested this on 10.9.70 and it works as advertised - I get a complete surface on the protein instead of a fragmented one. Yay! Further question: on your test page when you issue this command, the resulting surface has rounded "bumps". When I do it locally, the surface is "pointy" instead of rounded. You are using a cif file on the test site and I am using a pdb file. Is this a difference between Jmol handling of cif and pdb files? Or ?? Problem with JVXL data on Mac OSX: I cannot copy the contents of the Jmol script console to the clipboard. Therefore when I say show isosurface to get the JVXL data, I can see them but have no way to get them from the Jmol console into a file for later use. This is true for the app and the applet. I seem to recall that this is due to a problem with Apple's implementation of Java, and that on a Win machine you can copy/paste from/to the Jmol console. Any ideas on how to get around this problem on a Mac? (Note that on Mac OSX you can copy from the Jmol Console and paste into the Jmol Console - but not between apps). Bob Hanson wrote: > I'd be very interested in knowing > how other programs handle this. The program I can comment on for handling of surfaces is Chime. I recall that Chime ignored whatever was not selected when calculating a surface. I find that more intuitive - "just put a surface around whatever is selected" but perhaps there are reasons for using ignore () instead. In any case I am very glad to have surfaces implemented! Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |