Message: 5
Date: Wed, 4 Oct 2006 10:51:29 -0400
Subject: Re: [Jmol-users] surfaces and JVXL files
Content-Type: text/plain; charset="us-ascii"
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
