Re: [Jmol-users] surface calculation and rendering time

[Robert H. <ha...@st...>]

Jaim, I also suggest using

write isosurface "xxxx.jvxl"

from the Jmol application or signed applet. This only works if you
have a predefined notion of the surface you want to display; see notes
at

http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm

and

http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf

Basically, you just create the surface and write it to disk, then load
it with the isosurface command:

isosurface "xxxx.jvxl"

Bob






On Fri, Jan 30, 2009 at 7:52 AM, Karl Oberholser <obe...@me...> wrote:
> In settings other than Proteopedia I reduce the time required to display a
> surface by generating a data file of the surface, and then just display the
> surface rather than calculate the surface each time the script is run.  I do
> not think that there is a way to do this in Proteopedia, at least I have not
> discovered how to do it if it is possible.
>
> Karl
>
>>>> <lsp...@we...> 1/30/2009 12:21 AM >>>
> Hi,
>
> Is there a way to reduce the time required for Jmol for generating
> and rendering surfaces?
>
> Can we optimize the script data to help Jmol, ie: store the coordinates in
> the script on a better order, select atoms in a better way, pre-calculate
> something ?
>
> Thanks in advance,
> Jaim
> --
> Dr Jaime Prilusky                      | Jai...@we...
> Head of Bioinformatics ISPC            |
> R&D Bioinformatics and Data Management |
> Weizmann Institute of Science          | fax: 972-8-9344113
> 76100 Rehovot - Israel                 | tel: 972-8-9344959
>
> OCA, http://oca.weizmann.ac.il (the protein structure/function database)
> Proteopedia, http://www.proteopedia.org (because life has more than 2D)
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900