Thanks to all for the help so far. I'm getting there, but am currently
pondering
about the definition of the palette_dict. I wanted to add a color gradient
such
as grey_yellow, as the green_yellow didn't work as well as I was hoping for.
I'm not entirely sure what the color codes refer to.
i.e.
'yellow_blue' : ('c',3, 0, 83),
'blue_yellow' : ('c',3, 83, 0),
What do the parameters 'c', 3, 0 and 83 refer to, respectively? And is there
a
quick way to find the correct numbers matching a certain color for a
customized
gradient? Thanks for any further help.
Peter
--
Dr Peter Teriete
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Rd.
Oxford
OX1 3QU
Tel: +44 1865 275742
Fax: +44 1865 275182
"count" is the operator you're looking for:
spectrum count, green_yellow, selection=50-100/
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist, DeLano Scientific LLC,
400 Oyster Point Blvd., Suite 213,
South San Francisco, CA 94080
Biz:(650)-872-0942 Tech:(650)-872-0834
Fax:(650)-872-0273 Cell:(650)-346-1154
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Charles Moad
> Sent: Tuesday, November 02, 2004 11:26 AM
> To: Peter Teriete; pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Coloring gradient
>
> I think I can help you except for one part. In short you
> want the 'spectrum' command. For example, you can color a
> chain R, based on the b-factor with the command:
>
> spectrum b, green_yellow, chain R
>
> The problem is that you must color based on a numeric value
> that each atom has associated. So let's say you want to
> color a helix from residue index 300-400. I tried:
>
> spectrum resi, green_yellow, resi 300-400 spectrum
> resi_number, green_yellow, resi 300-400
>
> ...and several other variations without success. Somebody
> out there might no the answer to this problem.
>
> -Charlie
>
> Peter Teriete wrote:
> > Dear All,
> >
> > I'm trying to color a protein cartoon structure from N- to
> C-terminal
> > with a green to yellow gradient. Had a browse around and couldn't
> > quite find the correct command. Any pointers are welcomed.
> >
> > Peter
> >
>
>
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