Re: [PyMOL] Rotation of a Protein

[Thomas H. <sp...@us...>]

Hi Kanika,

you can do this with the "rotate" command, without any additional script 
(like Michael already suggested). Note: for a dimer the the center of 
mass does not yet define an axis, my example uses an arbitrary axis on 
the mirror plane between the monomers.

# get some homodimer
fetch 3p8d, dimer, async=0

# create copies of one monomer
create copy1, dimer and chain A
create copy2, dimer and chain A
create copy3, dimer and chain A
create copy4, dimer and chain A

# orient will put the (unweighted) center of mass in the middle of
# the window and both monomers on the camera x-axis
orient dimer

# now rotate around the z-axis in camera space
rotate z, 60, copy1
rotate z, 120, copy2
rotate z, 180, copy3
rotate z, 240, copy4

Have a look at:
http://pymolwiki.org/index.php/Orient
http://pymolwiki.org/index.php/Rotate

If you need more fine control, go for Troels suggestion. There are also 
center-of-mass scripts on the PyMOLWiki.

Cheers,
   Thomas

kanika sharma wrote, On 10/09/11 07:47:
> I need to rotate the second unit of the dimeric protein on the line 
> joining their center of masses. rotate it at a atep of 60 degrees till 
> 240 degree..
> 
> 2011/10/8 Troels Emtekær Linnet <tl...@gm... 
> <mailto:tl...@gm...>>
> 
>     If you need rotations around an line, instead of axis, check out
> 
>     http://www.pymolwiki.org/index.php/Rotkit
> 
>     Troels Emtekær Linnet
>     Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/>
>     04107 Leipzig, Tyskland
>     Mobil: +49 1577-8944752
> 
> 
> 
>     2011/10/7 kanika sharma <ksh...@gm...
>     <mailto:ksh...@gm...>>
> 
>         Hello everyone,
>         I Have a protein with 2 chains.
>         I have to rotate the second chain of the protein by
>         60,120,180,240 degrees each.
>         Is there a script in PyMol that can do that?
> 
>         Best,
>         Kanika

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen