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<mailto: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
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