Hi Brenton, Jared,
For RNA, the residue names are A, C, G, and U (not R*). However it's also
possible to specify the nucleic acid, using:
set cartoon_color, green, resn G and byres name C1'
This way, you filter the selection on an atom of the ribose, that is in all
nucleic acids, and in no amino acid.
Hope it helps,
Tsjerk
On Fri, Mar 27, 2015 at 6:34 AM, Sampson, Jared <jared.samp...@nyumc.org>
wrote:
> Hi Brenton -
>
> To avoid coloring e.g. Glycine when you only want to color e.g. guanine,
> prefix the residue name with “D” (as the residues are shown in the Sequence
> viewer) for DNA. I believe RNA works the same way with “R” as well.
>
> set cartoon_color, green, resn DG
>
>
> To color the DNA backbone, you could try:
>
> color pink, resn DA+DC+DG+DT and bb.
>
>
> or, if you know the chain IDs,
>
> color pink, 2XCT and chain A+B+C+D+E and bb.
>
>
> Hope that helps.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
> On Mar 24, 2015, at 11:47 PM, Brenton Horne <brentonho...@ymail.com>
> wrote:
>
> Hi,
>
> I've seen this (Example 1 on 3DNA
> <http://www.pymolwiki.org/index.php/3DNA>) and I noticed to colour each
> nucleic acid differently they used something like:
>
> set cartoon_color, green, resn G
>
> for each of the four different nucleic acids. When I ran this for 2XCT bio
> assembly 1 it coloured amino acids with the same single letter codes as the
> four nucleic acids (e.g., G for guanine [nucleic acid] and glycine [amino])
> and I wanted to know how to run it just for nucleic acids. I thought that
> something like this for each chain containing nucleic acids:
>
> set cartoon_color, green, /2XCT//E and resn G
>
> would do the trick but that would take forever seeing how 8 separate
> chains contain nucleic acids. While we're on this topic I'd also like to
> know how to colour the backbone and sugars via a more efficient method than
> doing something like this:
>
> color pink, /2XCT//E and bb.
>
> for each chain containing nucleic acids.
>
> Thanks for your time,
> Brenton
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for
> all
> things parallel software development, from weekly thought leadership blogs
> to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now.
> http://goparallel.sourceforge.net/_______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for
> all
> things parallel software development, from weekly thought leadership blogs
> to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Tsjerk A. Wassenaar, Ph.D.
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
