VMD-L Mailing List

From: Jennifer Williams (Jennifer.Williams_at_ed.ac.uk)
Date: Tue Apr 20 2010 - 10:13:04 CDT

Thanks for the help.

I've found a simple solution -probably should have tried it earlier...

It turns out I can just load and alter the initial .pdb file (I rename
SI as Z using find and replace) and colour the atoms by name. Once the
structure is looking as I'd like it to I then load the trajectory into
the structure and it doesn't seem to matter that the atoms names don't
match the first structure I loaded (i.e in the rest of teh frames SI
is not renamed to Z) but all frames keep the colouring of the initial
.pdb file I loaded.

Jenny

Quoting Jennifer Williams <Jennifer.Williams_at_ed.ac.uk>:

>
>
> Hi,
>
> I have a structure and need to change the colours of certain atoms. In
> my .pdb file I have SI and S. Both are automatically recognized as S in
> VMD and given the same colour. I am unable to change this using the
> colour control in the graphical interface.
>
> I know that I could easily do find and replace in my .pdb file but I
> also have trajectory files which I cannot format.
>
> Is there someone around this -perhaps using some script command. Any
> help greatly appreciated,
>
> Jenny
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861 

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.