[PyMOL] RE: Orient molecule

Steve,

This is something PyMOL can do with a little help from Python...
  
# PyMOL script: view2coord.pml

# get the current camera matrix
v=cmd.get_view()

# translate atoms to the current origin of rotation
alter_state 1, all, \
(x,y,z) = (x-v[12],y-v[13],z-v[14])

# apply the rotation (matrix multiplication)
alter_state 1, all, \
(x,y,z) = (x*v[0]+y*v[3]+z*v[6], \
x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8])

# end script

After loading a molecule and choosing a view (either with the mouse, or
using commands like "orient", "turn", "move", "center", etc.), you then
simply run the script and save the new coordinates:

load original_mol.pdb
orient
center 10/ca
@view2coord.pml
save transformed_mol.pdb
quit

Oh, and yes, PyMOL is still free unless you choose to pay for it.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: Computational Chemistry List 
> [mailto:che...@cc...] On Behalf Of Steve Bowlus
> Sent: Wednesday, June 23, 2004 8:42 PM
> To: che...@cc...
> Subject: CCL:Orient molecule
> 
> I am frantically searching for a simple piece of code that 
> will allow me to:
> 
> Read a standard file (mol, pdb, Sybyl ...) select an atom to 
> put at the Cartesian origin select an atom to put on the X 
> axis select an atom to put in the XY plane Do a rigid 
> rotation Do sequential rigid rotations about Cartesian axes 
> Freeze the molecule in the new orientation Output the NEW, 
> transformed coordinates.
> 
> This is equivalent to the Sybyl "orient" command, plus rigid 
> rotations, plus "Freeze molecule". But I have not found a 
> free (or even cheap) package that will freeze a molecule in 
> the new coordinates before output.
> 
> Thanks in advance for any pointers,
> Steve
> 
> 
> -= This is automatically added to each message by the mailing 
> script =- To send e-mail to subscribers of CCL put the string 
> CCL: on your Subject: line and send your message to:  
> CHE...@cc...
> 
> Send your subscription/unsubscription requests to: 
> CHE...@cc... 
> HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs 
> 
> If your mail is bouncing from CCL.NET domain send it to the 
> maintainer:
> Jan Labanowski,  jla...@nd... (read about it on CCL Home Page)
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+
> 
> 
> 
> 
> 
>