pymol-users

[PyMOL] Apply a transformation matrix to a selection

[<ser...@gm...>]

Hi people!

I'm trying to apply a transformation matrix to a few atoms in a
representation. By now I'm using a python script that modify the
position vector directly in the pdb, and then load the new pdb, but I
think that should exist some other way to apply the matrix direct with
the pymol.

Something like

   create a,resi 10
   apply_transformation_matrix a, [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]]

Or I'm just dreaming?

Thanks!

-- 
"Two of the most famous products of Berkeley are LSD and Unix. I don't
think that this is a coincidence."
http://servomac.blogspot.com

Re: [PyMOL] Apply a transformation matrix to a selection

[DeLano S. <de...@de...>]

Tony,

create a, resi

cmd.transform_selection("a", [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]],
homogenous=3D1)

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf=20
> Of Toni Piz=E0
> Sent: Thursday, January 31, 2008 9:45 AM
> To: pym...@li...
> Subject: [PyMOL] Apply a transformation matrix to a selection
>=20
> Hi people!
>=20
> I'm trying to apply a transformation matrix to a few atoms in=20
> a representation. By now I'm using a python script that=20
> modify the position vector directly in the pdb, and then load=20
> the new pdb, but I think that should exist some other way to=20
> apply the matrix direct with the pymol.
>=20
> Something like
>=20
>    create a,resi 10
>    apply_transformation_matrix a,=20
> [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]]
>=20
> Or I'm just dreaming?
>=20
> Thanks!
>=20
> --
> "Two of the most famous products of Berkeley are LSD and=20
> Unix. I don't think that this is a coincidence."
> http://servomac.blogspot.com
>=20
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[PyMOL] Fwd: Apply a transformation matrix to a selection

[T. P. <ser...@gm...>]

>  create a, resi
 >
 >  cmd.transform_selection("a", [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]],
 >  homogenous=1)


Thanks (is better late than never)!

 But I want to apply a set of selective transformations with a time
 between them (using the time.sleep() function of python), making the
 efect to the user that the molecule is animated. Therefore I can't use
 the create function, because it centers and zoom the new object
 created, and I doesn't want this.

 Anybody know how to apply a transform to a selection, without crating
 a new object? Or create a new object without zooming them?

Another subject... why this command outputs me an error?

cmd.transform_selection("all",
[[0.99,-0.116,-0.081,0.391],[0.119,0.993,0.027,0.321],[0.077,-0.037,0.996,0.233],[0.0,0.0,0.0,0.0]],
homogenous=1)

The result is

PyMOL>cmd.transform_selection("all",
[[0.99,-0.116,-0.081,0.391],[0.119,0.993,0.027,0.321],[0.077,-0.037,0.996,0.233],[0.0,0.0,0.0,0.0]],
homogenous=1)
CmdTransformSelection-DEBUG: bad matrix


-- 
"Two of the most famous products of Berkeley are LSD and Unix. I don't
think that this is a coincidence."
http://servomac.blogspot.com

Re: [PyMOL] Fwd: Apply a transformation matrix to a selection

[Robert C. <rob...@qu...>]

Hi Toni,

On Tue, 04 Mar 2008 13:01:58 +0100, Toni Pizà <ser...@gm...>
wrote:

> >  create a, resi
>  >
>  >  cmd.transform_selection("a", [[x,x,x,x],[x,x,x,x],[x,x,x,x],[x,x,x,x]],
>  >  homogenous=1)
> 
> 
> Thanks (is better late than never)!
> 
>  But I want to apply a set of selective transformations with a time
>  between them (using the time.sleep() function of python), making the
>  efect to the user that the molecule is animated. Therefore I can't use
>  the create function, because it centers and zoom the new object
>  created, and I doesn't want this.
> 
>  Anybody know how to apply a transform to a selection, without crating
>  a new object? Or create a new object without zooming them?

If you set the variable auto_zoom to 0, then PyMOL will not zoom to a new
object.  I set this in my .pymolrc file, because I prefer to always zoom when
I want.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc