My software notes

May 24, 2012

[PyMOL] different colors of nucleic acid rings

Filed under: pymol/ molmol — kpwu @ 12:55 am
Tags: , ,

The image below can be drew followed by steps in my earlier post, which shows single color of the nucleotide rings and bonds.

I saw a discussion list at PyMol forum today that an user requested a way to display different colors of the nucleotide rings. Below is the example image I tested (using PDB: 2WCC).

One thing to note: if you use “set cartoon_ring_color, xxx” in the beginning, you may not see your ring/bond in same color. Then you have to do one more step to color the bond color by using “color red, resn A (or DA, or other nucleic acids)”.

Pymol commands:

fetch 2WCC
as cartoon
bg_color white
select DNA, ///1 + ///2
cartoon oval, DNA
set cartoon_ring_mode, 3
set cartoon_nucleic_acid_color, blue
select dna_A, resn DA (here the Adenosine is named as DA)
select dna_C, resn DC
select dna_G, resn DG
select dna_T, resn DT
color yellow, dna_A
color red, dna_C
color gray40, dna_G
color palecyan, dna_T

* The 4 select can be skipped and use “color yellow, resn DA” in the coloring steps.

**IF you use “set cartoon_ring_color, orange” for all nucleotides in the beginning and wanna change colors for specific types of nucleotide rings, you may meet problems that command “set cartoon_ring_color, red, resn DA” (for the rings) and “color red, resn DA” (for the bonds in sidechain) don’t work sometimes. I somehow can change the bond color but not always (don’t know why– it works on my macbook but no on my iMac, both are MacPyMOL).

Advertisements

1 Comment »

  1. […] May 24, new post about different colors for the rings. Like this:LikeBe the first to like this post. Comments […]

    Pingback by [PyMOL] DNA–example II « My software notes — May 24, 2012 @ 12:59 am | Reply


RSS feed for comments on this post. TrackBack URI

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Create a free website or blog at WordPress.com.

%d bloggers like this: