[Molvis-list] How to superpose two molecules in a molecular viewer?

[Timothy Driscoll]

On May 18, 2007, at 12:29 AM, Julio Cesar da Silva wrote:

>
> I have a doubt about how to superpose two molecules in a molecular  
> viewer.
> I need to superpose two protein structure in a spacefill  
> representation. I
> would like to show one of them with semi-transparency. I have tried  
> to do
> this in the softwares Rasmol and Pymol, but I could not. I would  
> like to
> show both of them at same time and can see both. So, I would like  
> to show
> one semi-transparent and the other one normal. Please, does someone  
> know
> how to do this? Could you help me? Thanks.
>
hi Júlio,

I'm sure many programs can do what you want.  here is how to do it in  
Jmol:

launch Jmol.app and bring up a scripting window.
then issue the following commands (for example):


# use the 'load files' command to load multiple files

load files "file1.pdb" "file2.pdb"


# file1.pdb can be accessed as model 1.1
# use the 'color translucent' command to control translucency of atom  
spheres

select model=1.1
wireframe off
spacefill 100%
color cpk
color translucent 0.5


# file2.pdb can be accessed as model 2.1

select model=2.1
wireframe off
spacefill 100%
color cpk


# note: the 'select' command does NOT change what is displayed!
# use the 'model' command to toggle display.

# show only model 1.1
model 1.1

# show only model 2.1
model 2.1

show all models
model 0


Jmol has a number of animation controls as well; check out the  
interactive documentation (esp. the 'frame' command) for all the  
details:

<http://www.stolaf.edu/academics/chemapps/jmol/docs/>



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

04-16-07.  We will not forget you.