RE: [PyMOL] Coloring "ladder" differently from "ribbon" in nucleic acid representation

[Warren D. <wa...@de...>]

Alex,

Hmm...not exactly.  you could set a uniform cartoon color for an object
and then color the residue on a per-atom basis, or vice versa by setting
the cartoon_ladder_color and relying on the atomic color for the
cartoon, but there isn't a specific per-residue ladder or cartoon color
(yet).

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Alex Luso
> Sent: Wednesday, December 14, 2005 7:01 AM
> To: pym...@li...
> Subject: [PyMOL] Coloring "ladder" differently from "ribbon"=20
> in nucleic acid representation
>=20
>   Hi,
>=20
>   The new nucleic acid representation options are very welcome.
>=20
>   One question regarding the coloring of the ladder
> "sticks":
>=20
> If I am in:
> cartoon_nucleic_acid_mode, 1
> cartoon_ladder_mode, 1
> cartoon_ring_mode, 0
>=20
> Is there a way to color the stick of a specified nucleotide=20
> differently from its ribbon?=20
> I can get a gradient color for the stick by doing "color=20
> green, /object///res/N1"
> but if I try to change the color of the other atom involved=20
> in the ladder "stick" (i.e. "color green,=20
> /object///res/C3*"), then the color of the ribbon changes too=20
> (because we are in cartoon_nucleic_acid_mode,1). It's clearly=20
> possible to do b/c I can change the color of all sticks by=20
> doing "set cartoon_ladder_color, green" but this command acts=20
> globally.
> I guess a related point is that perhaps it would be better to=20
> control the color of cartoon components directly, and=20
> selectively, rather than through the indirect method of color=20
> of atom -> maps to color of stick.
>=20
>   Anyway, great job of integrating cartoon ribbons and the=20
> various ladder and ring options for nucleic acids. They look=20
> great. I am sure other options are on the way (as well as=20
> actual documentation!!).
>=20
>   -Alex
>=20
> BTW: the wiki is wrong in
> http://www.pymolwiki.org/index.php/Examples_of_cartoon_ring_an
> d_cartoon_ladder_settings
> where it says that cartoon_nucleic_acid_mode,1 # follows=20
> phosphates. That should read # follows C3*, as far as I can tell.
>=20
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection=20
> around http://mail.yahoo.com=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20