[PyMOL] Default colors by element

[S. Frank Yan]

Hi,

Is there anyway to show the default color scheme of different elements?
The basics such as CHNOS are clear, but how about F, Cl, Br, I, P, Na,
Mg, Ca, etc?

Thanks a lot,
Frank

[Robert Campbell]

Hi Frank,

Post by S. Frank Yan
Is there anyway to show the default color scheme of different elements?
The basics such as CHNOS are clear, but how about F, Cl, Br, I, P, Na,
Mg, Ca, etc?

In the "Settings" menu on the external GUI, you can select "Colors..."
Then you will get a box with all the colours listed in it. You can
select a colour and then the "Edit" button (or just double click the
colour name) to see the colour.

Otherwise you can look in the source in the file: layer1/Color.c
to see the complete colour listing at once.

Cheers,
Rob

[Warren DeLano]

Note also that PyMOL beta versions now match Jmol's colors
element-for-element except for those few atomic colors previously defined in
PyMOL (just C,N,O,H,S -- I think)

Changing those colors is simply a matter of changing the associated color
name:

set_color helium, [ 0.4, 0.3, 0.7]
recolor

Carbons are the only exception, siince objects in PyMOL are given one of 40
default carbon colors in a repeating cycle so that separate molecules can be
visually distinguished. To turn this off:

set auto_color, off

To get a Jmol-like carbon:

set_color carbon, [0.564, 0.564, 0.564]

load some_pdb_file.pdb

Cheers,
Warren


--
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:[phone] Cell:(650)-346-1154

-----Original Message-----
Robert Campbell
Sent: Thursday, February 03, 2005 10:20 AM
Subject: Re: [PyMOL] Default colors by element
Hi Frank,

Post by S. Frank Yan
Is there anyway to show the default color scheme of

different elements?

Post by S. Frank Yan
The basics such as CHNOS are clear, but how about F, Cl,

Br, I, P, Na,

Post by S. Frank Yan
Mg, Ca, etc?

In the "Settings" menu on the external GUI, you can select "Colors..."
Then you will get a box with all the colours listed in it.
You can select a colour and then the "Edit" button (or just
double click the colour name) to see the colour.
layer1/Color.c to see the complete colour listing at once.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
613-533-6821
613-533-2497
Kingston, ON K7L 3N6 Canada
http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5
F635 C0E2
-------------------------------------------------------
This SF.Net email is sponsored by: IntelliVIEW -- Interactive
Reporting Tool for open source databases. Create drag-&-drop
reports. Save time by over 75%! Publish reports on the web.
Export to DOC, XLS, RTF, etc.
Download a FREE copy at http://www.intelliview.com/go/osdn_nl
_______________________________________________
PyMOL-users mailing list
https://lists.sourceforge.net/lists/listinfo/pymol-users