[Molvis-list] label molecules using Jjmol

[Timothy Driscoll]

On Mar 8, 2007, at 5:46 AM, S.S. Gong wrote:

> Dear all,
>
> "label" which is a command of rasmol scripts draws default atom  
> labels.
> I just want to label not for very atom but for a selected residue  
> or an amino acid.
>
> "label residue true", which is a command of labeling a selected  
> residue, works well witch Chime but not with Jmol.
> It would be better if I could label selected molecules using  
> 'define' command.
> Any tips for labeling not for every atom but for defined regions or  
> a selected residue with Jmol?
>
hi,

Jmol has a lot of label options; see

<http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#label>

like Rasmol and Chime, in Jmol, labels are attached to specific  
atoms.  the content of the label can be textual:

select *.ca and 43A
label "My Favorite Carbon"


or it can be contextual:

select *.ca
label %m  # labels all alpha-carbons with the 3-letter code of their  
parent residue


this latter method can be used to label by residue. (use %n for the 1- 
letter codes.)



hope that helps,

tim
-- 
Timothy Driscoll                                em: molvis at vbi.vt.edu
Virginia Bioinformatics Institute               ph: 540-231-3007
Bioinformatics I: M-1                           im: molvisions
Washington St., Blacksburg, VA 24061