My software notes

May 2, 2013

[PyMOL] molmol-like colors on secondary structural elements

Filed under: pymol/ molmol — kpwu @ 9:18 pm
Tags: ,

I  recently saw some nice presentations of protein structures prepared by MOLMOL. Since MOLMOL is not actively maintained,  I wonder how to make similar colors on the secondary structural elements in PyMOL.

In this short blog,  an example is shown. The top and bottom figures  are made by PyMOL and MOLMOL, respectively.

How I did that? Basically, just make highlight color yellow, turn on discrete cartoon color, adjust the width and length of strands.

The PyMOL script is shown here, too:

cmd.show_as(“cartoon” ,”all”)
bg_color white
set cartoon_highlight_color, yellow
set cartoon_rect_width, 0.03
set cartoon_rect_length, 1.7
set cartoon_discrete_colors, on
util.cbss(“all”,”red”,”cyan”,”gray70″,_self=cmd)

2H28-molmol like

x

Advertisements

1 Comment »

  1. You’re entitled to your opinion about the singing. As far as the issue of Josh Groban and what he knows about the problems Africans face today, you may want to do a bit of research before mouthing off. Obviously Nelson Mandela felt strongly enough about Josh’s knowledge of his country’s problems and his ability and desire to make a difference, that he made him an ambasssador for his Aids Foundation. Some of the contributions from GFC, Josh’s charitable foundation, goes to helping children in Africa as well as here. You may not like his voice, but you cannot assassinate his character; this young man is using his celebrity to help others. Some of the other young celebrities that live in the tabloids should take a lesson from Josh Groban. Come on http://tropaadet.dk/salinasmullen40682081845

    Comment by salinasmullen40682 — April 8, 2016 @ 5:50 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

Blog at WordPress.com.

%d bloggers like this: