[Chimera-users] changing the content and colour of labels

Sumitro Harjanto sharjanto at i2r.a-star.edu.sg
Tue Oct 5 20:27:04 PDT 2010

Hi Elaine,


Regarding point (2): changing the content of the label, other than using
the gui menu, can I do it through command line?


I am dealing with quite a large number  of residues for labeling. So if
I can automate the process through scripting will be good. 


I came across this command rlabel which allows me to label the residues,
but it seems to, by default, print out labels with both residue position
along the chain and 3-letter code, which I would like to omit. I read
its documentation but doesn't seem to allow me to change the content of
the label printed out through this command.


I am exploring labelopt also, but I am not too sure if it is helpful.


Please advise, thanks! =]







From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, October 06, 2010 12:10 AM
To: Sumitro Harjanto
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] changing the content and colour of labels


Hi Sumitro,

1. yes, you can change the color of the labels only, using either the
"Actions... Color" menu or the color command.


If menu, in version 1.5 (daily build), choose "Actions... Color... all
options" and in that dialog set "coloring applies to" to "residue
labels" and then do the coloring. In earlier versions, choose
"Actions... Color... residue labels" and then use that menu again to do
the coloring.  Either version, you should probably change back from
"residue labels" to "all of the above" again after coloring the labels
to avoid later confusion. 


If command, you would just put a modifier right after the color name.
Modifiers include ",l" (letter ell) for labels, ",lr" for residue
labels, etc. as documented here:


Example: color hot pink,lr :52

to color residue label only of residue 52 hot pink.  No space after the


2. yes, use menu item "Actions... Label... Residue... custom"  to set
custom residue label contents. Documented here:






Elaine C. Meng, Ph.D. 

UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab

Department of Pharmaceutical Chemistry

University of California, San Francisco


On Oct 5, 2010, at 3:14 AM, Sumitro Harjanto wrote:

Hi Elaine,

Thanks for your prompt reply on the previous issue. I have managed to
get the colours on the residues.

Now I have another problem pertaining to the label.


1.       Is there a way to change the colour of the label such that it
is different from that of the residue..?

2.       How can I change the information on the label such that only
the residue's position is shown (omitting the residue's name/type)? 





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