[Chimera-users] Display Molecule Name

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 3 10:45:27 PDT 2009

Hi Chris,
We thought of a way.  You can use the "labelopt" command to set atom  
labels to any atom attribute, and "molecule" is an atom attribute.

Example commands:

open 1g1p
rainbow models
[ then I used the "Tile Structures" tool to spread the structures out ]
labelopt info molecule
la @/serialNumber=1

That shows labels like:  #0.14
1g1p is an NMR ensemble, just an example with 18 submodels (in this  
case #0.1-18).  You would only want to label one atom per model since  
all the labels in a given model would be the same.  I just labeled  
the atom with serial number 1, but you could use a different serial  
number, or some other specifier that you know will match one atom per  

I guess the trickiest thing would be to get an atom at the periphery  
of the model so that the label is easily viewed instead of embedded  
in the structure.

You could even get a label like:  molecule #0.14
The easiest user interface way to get that would be to select one  
atom or one residue per model (e.g. "select @/serialNumber=1") and  
choose menu item "Actions... label... residue... custom" and in the  
resulting dialog, specify the Residue label as

molecule %(molecule)s

You could include leading spaces to move the label to the right.  As  
with the custom atom labels, a limiting factor is not much control  
over label placement.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 2, 2009, at 11:02 PM, cdlau at ucsd.edu wrote:

> Hi,
> Thanks for the response.  This would not work for my case because I am
> writing a plugin for ViewDock for use with a Tiled Wall Display.  I  
> was
> hoping there was a setting that was available to show the molecule  
> name
> (if a setting does exist I can initiate it with runCommand).  Does  
> anyone
> know if this is possible?
> Thanks,
> Chris
> On Thu, 2 Jul 2009, cdlau at ucsd.edu wrote:
> Hi,
> I was wondering if there was a way to display the molecule name  
> that is
> being shown in chimera.  A simple display such as "molecule #0.10"  
> below
> the rendered molecule would be great.
> Thanks for your help,
> Chris
> Just place the mouse over the item you want to know more about and  
> a popup
> balloon will tell you about it.  The text starts with the model  
> number,
> e.g., #0.10, and may or may not have additional information, i.e.,  
> for an
> atom it includes the residue name and sequence number and the atom  
> name.
>        - Greg
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list