VMD-L Mailing List

From: Mark Cunningham (cunningham_at_utpa.edu)
Date: Tue Jul 19 2011 - 15:19:53 CDT

Darrell:

You can assign different carbon colors to Name and to Type and to Element.
You can then color different selections according to Coloring Method: Name or Type or Element.
This will give you at least three different representations that color most atoms by
their "normal" colors and carbon differently. You can also hijack the other
Coloring Methods if you need more than three different colors of carbon but those
may require more work to put the other atom colors back to their "normal" colors.

Mark
________________________________________
From: Hurt, Darrell (NIH/NIAID) [E] [darrellh_at_niaid.nih.gov]
Sent: Tuesday, July 19, 2011 2:24 PM
To: Mark Cunningham; maria goranovic
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: shades of licorice representation

Hi everyone,

Mark's answer is exactly what Maria was asking for and provides a "look and feel" of PyMOL to VMD. However, I wonder if Maria also wants the "PyMOL-like" ability to have different molecules (structures) colored differently in the scheme she has described. I think that Mark's answer will color every "C" name in every molecule the same color (whether the default cyan or some other color), which will make distinguishing different molecules difficult if they are overlaid. Is there some way to color the carbon atoms of one molecule differently than the carbon atoms of another molecule while keeping ALL of the oxygen, nitrogen, sulfur, etc. atoms in every molecule colored in their traditional, default colors?

Thanks,
Darrell

Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62G, MSC 2135
Bethesda, MD 20892-2135
Office 301-402-0095
Mobile 301-758-3559
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From: Mark Cunningham <cunningham_at_utpa.edu<mailto:cunningham_at_utpa.edu>>
Date: Tue, 19 Jul 2011 12:53:54 -0400
To: maria goranovic <mariagoranovic_at_gmail.com<mailto:mariagoranovic_at_gmail.com>>
Cc: "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>" <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: RE: vmd-l: shades of licorice representation

 Maria:

The VMD licorice representation does exactly what you want, or at least
exactly what is shown in the figure you sent. To change the carbon color,
go to the Graphics..Colors menu. Select the Category Name and Name C,
then choose the color you want for carbon. If you select pink for carbon,
then VMD will draw a bond that is half pink and half blue (if connected to
nitrogen). If it is still somehow cyan, then you have TWO representations
that are drawing the bond. Delete the other representation.

Mark
________________________________
From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] on behalf of maria goranovic [mariagoranovic_at_gmail.com<mailto:mariagoranovic_at_gmail.com>]
Sent: Tuesday, July 19, 2011 7:53 AM
To: VMD list
Subject: vmd-l: shades of licorice representation

Hi

I am wondering if this feature is already present in VMD?

In Pymol, it is possible to color an amino acid residue represented as licorice in say, orange, and yet one can distinguish between different atoms of the residue. For example, all bonds will become pink, but a nitrogen will still appear blue and an oxygen red. If I try to color all carbons in VMD pink, a C-N bond still appears in the cyan color, and the effect is not the same.

Such a representation can be very useful in visualization. for example:

http://hwmaint.jbc.org/cgi/content/full/285/34/26245/F4 

--
Maria G.
Technical University of Denmark
Copenhagen