Re: [PyMOL] Coloring of helices

[Folmer F. <fo...@gm...>]

Hi Markus,

As Andreas already mentioned, the cartoon color is taken from the color of
the CA atoms. So you could just color those differently and that should be
reflected in the cartoon colors.

But I think a better option is to use the cartoon_color command.
http://www.pymolwiki.org/index.php/Cartoon_color

I've just tried it on 1.4.1, and expect any recent PyMOL's to behave the
same.

Hope this helps,
Folmer


2014-08-22 0:33 GMT+02:00 Markus Heller <mh...@cd...>:

> Hi all,
>
> I'm stuck.  I'm trying to create a figure where I show a helix bundle,
> with select side chains shown as sticks.  I would like the helices to be
> green, and the side chains in different colors.  Easy enough, *but* the
> carbon color of the side chains supersedes the green color of the helices.
>
> I tried to duplicate the object and show sticks for one objects and
> helices for the other, which works in terms of color, *but* now the
> cartoon_side_chain_helper doesn't work, since I'm displaying sticks and
> helices from 2 different objects.
>
> How do I go about this?
>
> Thanks and Cheers
> Markus
>
> PS: Here's my attempt:
>
> # reset everything
> delete all
>
> # white background
> bg_color white
>
> # show valences
> set valence, 1
>
> # show valences inside rings, 0 = centered, 1 = inside
> set valence_mode, 1
>
> # antialias
> set antialias = 1
>
> # don't show backbone for cartoons
> set cartoon_side_chain_helper, on
>
> # keep standard helix, strand, loop representations
> # other options: cartoon loop, cartoon rect,
> # cartoon oval , cartoon tube
> cartoon automatic
>
> # Molscript-like edges for helices
> set cartoon_fancy_helices = 1
>
> # color inside of helices gray
> set cartoon_highlight_color, gray
>
> # load the PDB file
>
> load example.pdb, EXA
>
> # duplicate protein
> copy EXA_dup, EXA
>
> # hide everything
> hide everything
>
> # select protein
> select prot, polymer
>
> # show cartoon ribbon
> show cartoon, EXA
>
> # select helices
> select heli, (ss h and EXA)
> select heli_dup, (ss h and EXA_dup)
>
> # color everything limon
> color limon
>
> # select residue of interest
> select V27, (resi 27 and EXA)
> select S31, (resi 31 and EXA)
> select A34, (resi 34 and EXA)
> select H37, (resi 37 and EXA)
> select W41, (resi 41 and EXA)
>
> # show sticks for ROIs
> show sticks, (V27 or S31 or A34 or H37 or W41)
>
> # color ROIs
> color atomic, (V27 or S31 or A34 or H37 or W41)
> color yellow, (name C* and V27)
> color orange, (name C* and S31)
> color cyan, (name C* and A34)
> color magenta, (name C* and H37)
> color purple, (name C* and W41)
>
> # color helices properly
> show cartoon, EXA_dup
> color limon, EXA_dup
>
> # deselect all to avoid little pink squares
> deselect
>
> --
> Markus Heller, Ph.D.
> NMR Scientist
> CDRD - The Centre for Drug Research and Development
> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604)
> 827-1147
> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mh...@cd... |
> www.cdrd.ca
>
>
>
>
>
>
> Follow us:
>
> This email and any files transmitted with it are confidential and intended
> solely for the addressee.  If you are not the named addressee you should
> not disseminate, distribute, copy, or alter this email.
>
>
>
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Folmer Fredslund