Re: [Jmol-users] surfaces and JVXL files

[Frieda Reichsman]

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 ///////////////////////////////////////////

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