Dear Otello,
That should be possible right now. Basically what you are asking for is an
export of a surface to a file. It may not be in exactly the format you
desire, but it should be close. Let me think.... Basically what you would do
is display ONLY the surface, then use the WRITE command to create a file
with the information you want. For example:
isosurface.....
display none # doesn't affect isosurface, just atoms
write "t.vrml"
The VRML format is pretty simple -- just a list of vertices followed by a
list of triangles. I'm sure you can figure it out. Would that be enough?
The grid spacing is set using the RESOLUTION parameter for the isosurface
command.
isosurface resolution 10 sasurface
Just use the command
isosurface LIST
to see the number of vertices and triangles. Really high resolution for an
entire protein may not be feasible, so you might need to make careful use of
SELECT and IGNORE parameters.
Also, you know about the VOLUME and AREA parameters to the isosurface
command, right? Just in case that's all you are interested in.
Bob Hanson
On Mon, Nov 22, 2010 at 8:14 AM, Otello Maria Roscioni <
[email protected]> wrote:
> Dear Jmol-users and developers,
>
> I am writing you to share the settings that give the correct molecular
> surface for a periodic slab. Suppose you have a slab model of a surface
> with cell vectors {2.9 6.5 50.}, then the molecular surface computed with
> the correct boundary conditions is given by:
> $ load "slab.pdb" {3 3 1}
> $ isosurface slab within [{2.9 6.5 40.}. {0. 0. 100.}, {0. 6.5 0.}, {2.9
> 0. 0.}] solvent 1.8 lattice {1 1 1}
>
> As I would like to carry out calculations on a grid of points
> corresponding to this surface, I am wondering if there is a way to export
> such a grid in a convenient format. Ideally the grid should be a list of
> points ordered in this way:
>
> x1 y1 z1
> x1 y2 z2
> x1 y3 z3
>
> x2 y1 z4
> x2 y2 z5
> x2 y3 z6
>
> x3 y1 z7
> x3 y2 z8
> x3 y3 z9
>
> and there should be a possibility to chose the grid finesses in terms of
> XY spacing. Would be such a feature implemented in one of the future
> versions of Jmol?
>
> Thank you,
> Otello
>
>
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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
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
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