Vincent --
pqr format.
The column of data probably goes in as "partialcharge" data. I'd have to
verify that, but if that were the case, what you would do is simply:
load xxx.pqr
{*}.radius = {*}.partialcharge.all
isosurface sasurface 0
That should create a surface with a zero-radius probe (that is, "van der
Waals" radius) around those points.
If you want some subset of that surface, you would use, for example:
isosurface select(atomno < 30) sasurface 0
To combine this with a model, you would use:
load FILES "mymodel.pdb" "xxx.pqr"
frame 2
{*/2.0}.radius = {*/2.0}.temperature.all
isosurface sasurface 0
frame 0
or, after the fact:
load "mymodel.pdb"
....[later]...
load APPEND "xxx.pqr"
frame 2
{*/2.0}.radius = {*/2.0}.temperature.all
isosurface sasurface 0
frame 0
and if you issue
frame 1
that would "turn off" the surface, while
frame 2
would only show the surface.
DX format. No, not yet -- let's get that in there. Should be easy to
implement, since it is just another data reader. Currently Jmol can read
Gaussian cube, Jaguar , EFVet, MRC, XPLOR, and APBS files. These are very
simple add-ons, just involving a few required methods:
protected int readVolumetricHeader()
protected void readTitleLines()
protected void readVoxelVectors()
protected void readAtomCountAndOrigin()
protected float nextVoxel()
I'll need a few example files -- point me to a URL or send a ZIP file to
hans...@stolaf.edu
Custom objects -- we have DRAW objects and MEASURE objects that pretty much
does what you are talking about. For more complex objects, we have PMESH and
ISOSURFACE. These probably do what you want, or could. You can set
measurements to them so that if atoms move, the measures automatically
update.
Bob
On Fri, Oct 16, 2009 at 2:52 AM, Vincent Le Guilloux <
vincent.le-guill...@univ-orleans.fr> wrote:
>
> Dear JMol users,
>
> I'm trying to represent ligand pocket in JMol. For this purposes, I've
> two pocket representation as input: PQR file that contains a set of
> so-called alpha spheres having a defined radis, and DX file format
> used by DataExplorer (see
> http://www.cs.wpi.edu/research/DataExplorer/tutorial/data.html), that
> defines a discrete grid, and that can be read by pymol, and much more
> efficiently in term of representation by VMD.
>
> I've two questions here:
>
> 1. I'm trying to render the alpha spheres volumes defined in the last
> column of the PQR format, color it according to the residue name, and
> make it sligntly transparent, but so far I haven't find the way to do
> so. Is it possible?
>
> 2. Does JMol can read DX format? This second way to represent pockets
> is related to electron density map, and is represented by this format.
>
> 3. In a more general way, if I want to add to a given model a custom
> object, say a sphere with a given radius for example, and if I want to
> render it (volume, transparency, surface, custom color), to link it
> with other objects with a distance criteria, to select neighbor
> atoms... what would be the best way to do so ? Or the best place to
> learn it actually ? (if any, I'm prepared to go through the source
> code!)
>
> That's it, thanks in advance!
> Vincent.
>
>
>
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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
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