RE: [PyMOL] q: discrete colors and adjacent cartoon segments

[DeLano, W. <wa...@su...>]

Bartholomeus,

You have run into limitations in PyMOL's handling of single objects.

The answer to both these questions is to split your molecule into =
multiple object and color/show independently.  Use the "create" command =
to make copies, and then use alter to reassign secondary structure codes =
where needed.

Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501



> -----Original Message-----
> From: Bartholomeus Kuettner [mailto:bku...@ep...]
> Sent: Tuesday, January 28, 2003 3:06 PM
> To: pym...@li...
> Subject: [PyMOL] q: discrete colors and adjacent cartoon segments
>=20
>=20
> Dear PyMol users,
>=20
> 1.
> I'm puzzled with a coloring problem while coloring a protein molecule
> accordingly to its secondary structure by using 'discrete=20
> color' option:
> If there are a helix and/or strand adjacent together (e.g.=20
> helix from 1-10
> and sheet from 11-20) the small pseudo-loop region between=20
> (arising from
> atoms between last Calpha of the helix and first Calpha of=20
> the strand) gets
> colored like the latter partner (maybe because of its color=20
> was defined at
> last). What I'd like to do is to color this small pseudo loop=20
> in a different
> color. I've tried to color the atoms between last Calpha and=20
> next Calpha
> (C,N) individually but there was no effect. It seems to me,=20
> that cartoon
> coloring only corresponds to Calpha positions. So, is there a=20
> way around to
> color cartoon regions between secondary structure elements as=20
> described
> before?
>=20
> 2.
> Is there a way to force PyMol to draw a cartoon which shows=20
> two different
> secondary strcuture elements (helix, strand) ending and=20
> beginning at the
> same residue? Maybe one can image a scenario where the N atom makes a
> strand-like conformation while the CO group of the same=20
> residue starts with
> a helix. In another program it is/was possible to assign=20
> helix and strand
> ending and beginning in the same residue but when I try to=20
> perfom with PyMol
> only the last partner is shown correctly while the first partner gets
> overrided in its last residue, e.g. cartoon "strand 1-10" and=20
> "helix 10-20"
> looks the same like "strand 1-9" and "helix 10-20". How one=20
> could circumvent
> this dilemma?
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> Many thanks in advance!
>=20
> Greetings,
> Bartholomeus
>=20
>=20
>=20
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