Hey :)
Just as sidenote, the spectrum command takes arbitrary color schemes. Just
combine colors separated by underscores. Also fun in combination with
set_color :)
Cheers,
Tsjerk
On Feb 14, 2017 5:46 PM, "Robert Campbell" <robert.campb...@queensu.ca>
wrote:
Hello Peleg,
I think there are other possibilities, but my data2bfactor.py script will
do that for you. You create a file with whitespace-separated columns
(spaces and/or tabs) in which each line contains:
chain resi resn name data
(i.e. chain, residue number, residue name, atom name and value to be
applied to the B-factor column).
The number can also be applied to the occupancy column instead if you want
to keep the B-factor intact.
Then you can use the spectrum command or my color_b.py script to colour
each atom according to the data value. My color_b.py script has a few more
options than the spectrum command, including the ability to define a custom
colour gradient scheme.
You can find my scripts here:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
Cheers,
Rob
On Tue, 2017-02-14 17:12 +0100, Peleg Bar-Sapir <pel...@gmail.com> wrote:
> Hello,
>
> I wish to write a script that will take the molecule loaded in PyMol,
> and color the molecule according to values I will calculate using the
> molecules' parameters (in the end there will be one floating number
> per atom). Then, I would like to display that using surface mode.
>
> Could anyone direct me to a way of doing that? I saw scripts coloring
> by atom type, but I'm not sure how to apply it for a molecule already
> loaded in PyMol.
>
> Best,
>
> Peleg
--
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
<robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
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