Re: [PyMOL] label bond type and molecule name

[Jason V. <jas...@sc...>]

Sebastian,

Here's some help on labeling:

# label all atoms with the object name (file name minus extension)
label *, model

# label by residue name
label *, resn

Your command,

label C10, resn

was a good guess, but that asks PyMOL to "label the atoms in the
object called 'C10' by their residue name".  What you want is, "label
residue 10's carbon atom with the name of the residue" which would be
slightly different syntax:

# label residue 10's carbon atom with the residue name
label 10/C, resn

I suggest you check out the label command and syntax on the PyMOLWiki
(http://pymolwiki.org/index.php/Label) and the concomitant Labeling
category (http://pymolwiki.org/index.php/Category:Labeling).  Also
type "help label" into PyMOL.

In a multi-mol2 file theres the object name (determined from the file)
and the molecule name determined from the title field in the mol2
file.  Each object is loaded into a new state.  Try hitting pink
forward button in the lower right hand corner of PyMOL to switch to
the 2nd conformation.  If you want each molecule in its own object
instead of its own state load the file with:

load example.mol2, multiplex=1

Now the label command will work as expected:

label *, model

Cheers,

-- Jason


2010/6/4 Sebastian Kruggel <kr...@ch...>:
> hi,
>
> thanks for the answers jason and michael.
>
>  > set valence
>
> is what i was actually looking for. as i forgot to attach my example last
> time, my second question wasn't quite clear i guess: the filename which i
> used to load my molecules (all included in one mol2 file) is not the one of
> the different molecules - and this name, which is ATU_flexx_047/8_sis in the
> attached example, i want to display because it would be useful to see it
> cycling over the molecules in the different frames.
>
> i tried eg
>
>  > label C10, resn
>
> to put the name of each molecule on the C3 (i guess it will be no problem to
> place the label elsewhere) but i only get the beginning of the name (ATU_f)
> - which isn't very useful, because it is the same in all the different
> molecules...
>
> is 'resn' the right idea or do anybody have another idea how i can get the
> full name?
> thanks in advance,
>
> sebastian
>
>
> --
> Sebastian Kruggel
> Institut für Pharmazie
> Bundesstr. 45 | Raum 112 (406)
> D 20146 Hamburg
>
> Tel:   +49 (0)40 42838-3626 (-3484)
> mail:  kr...@ch...
> http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html
>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120