Re: [PyMOL] colouring surfaces according to molecular properties

[madsen <ma...@cc...>]

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,
>=20
> * Anders Madsen <ma...@cc...> [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?
> >=20
> > E.g. by accessing the coordinates that define
> > the surface and assign a colour to each triangle
> > involved in the surface mesh?
>=20
> If you only need to colour it at the resolution of the atoms (as oppose=
d
> 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-facto=
r
> 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=
:
>=20
>   http://adelie.biochem.queensu.ca/~rlc/work/pymol
>=20
> Within that script, four functions are defined:
>   data2b_atom
>   data2b_res
>   data2q_atom
>   data2q_res
>=20
> 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.
>=20
> You just need to create a data file that looks like:
>=20
> 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
>=20
> etc.  (or omit the chain if not defined in your structure)
>=20
> or=20
>=20
> A 1 ALA data
> A 2 SER data
> A 3 PRO data
>=20
> etc. (again omit the chain if not defined).
>=20
>=20
> Cheers,
> Rob
> --=20
> Robert L. Campbell, Ph.D.                         <rl...@po...=
>
> Senior Research Associate                            phone: 613-533-682=
1
> Dept. of Biochemistry, Queen's University,             fax: 613-533-249=
7
> Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rl=
c
>     PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2
>=20
>=20
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--=20
Anders =D8stergaard Madsen                         =20
Centre for Crystallographic Studies                =20
Department of Chemistry, University of Copenhagen  =20
Universitetsparken 5 DK-2100 KBH Denmark           =20
home: R=F8de Mellemvej 18, 1. DK-2300 Kbh. S         =20
email: ma...@cc... =20