Hi Anders,
With cmd.get_povray() (i.e. cmd.get_povray()[1]) you'll
get all vertex-coordinates describing the surface, but I
wouldn't know how you could use it to map something on
there neatly.
Cheers,
Tsjerk
On Wed, 22 Jun 2005 08:55:05 +0200
madsen <mad...@ccs.ki.ku.dk> wrote:
Dear Robert, Tsjerk, Jean-Philippe and Tim
thanks for your replies.
The colouring of atoms according to B-factors
or some other property is nice, but I really need
sub-atomic resolution of the properties that I would
like to map on the surface.
So, as Jean-Philippe and Tim are discussing, I would
like
to access the defining coordinates of the surface, or by
some
other means be able to hack the colouring of the
surface.
There is apparantly no standard trick for doing just
that.
I will have a look at povscript+.
Thanks for the hint!
regards
Anders
On Tue, Jun 21, 2005 at 02:23:24PM -0400, Robert
Campbell wrote:
Anders,
* Anders Madsen <mad...@ccs.ki.ku.dk> [2005-06-21 16:33]
wrote:
> Dear PyMol users,
> I would like to colour the beautiful
> PyMol molecular surfaces according to
> properties of the atoms involved.
> Has anyone experimented with this?
>
> E.g. by accessing the coordinates that define
> the surface and assign a colour to each triangle
> involved in the surface mesh?
If you only need to colour it at the resolution of the
atoms (as opposed
to individual surface vertices), then you can do so by
altering the
B-factor or occupancy values and colouring the structure
on those. I
have a script for reading a file of data and applying it
to the B-factor
or occupancy. Then you just need to colour using the
built-in spectrum
method or using my color_b.py script. See the
data2bfactor.py script in:
http://adelie.biochem.queensu.ca/~rlc/work/pymol
Within that script, four functions are defined:
data2b_atom
data2b_res
data2q_atom
data2q_res
The "2b" functions alter the B-factor and the "2q"
functions alter the
occupancy. The "_atom" functions are used to apply a
value to
individual atoms, while the "_res" functions are used to
apply a single
value to the whole residue.
You just need to create a data file that looks like:
A 1 ALA N data
A 1 ALA CA data
A 1 ALA C data
A 1 ALA O data
A 1 ALA CB data
etc. (or omit the chain if not defined in your
structure)
or
A 1 ALA data
A 2 SER data
A 3 PRO data
etc. (again omit the chain if not defined).
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
<r...@post.queensu.ca>
Senior Research Associate
phone: 613-533-6821
Dept. of Biochemistry, Queen's University,
fax: 613-533-2497
Kingston, ON K7L 3N6 Canada
http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238
A8F5 F635 C0E2
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Anders Østergaard Madsen
Centre for Crystallographic Studies
Department of Chemistry, University of Copenhagen
Universitetsparken 5 DK-2100 KBH Denmark
home: Røde Mellemvej 18, 1. DK-2300 Kbh. S
email: mad...@ccs.ki.ku.dk
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