pymol-users

[PyMOL] Multiple origins possible?

[Jon M. <jr...@co...>]

Hi all,

I'm new new to PyMol, but have a question so would appreciate any 
pointers people have. I currently read in a molecule to pymol, 'copy' 
it, and color the two copies at different positions. I set a single 
origin, being the centre of gravity of the combined molecules. Ideally, 
I'd like to be able to set two origins, and have the molecules rotate 
synchronously side-by-side rather than as one object, so I can compare 
more easily. Is this possible with PyMol?

Thanks,

Jon

-- 

Smart Bomb: "Cogito Ergo Boom."


###########

Jonathan Manning
PhD Student
Barton Group
School of Life Sciences
University of Dundee
Scotland, UK
Tel +44 1382 388707

RE: [PyMOL] Multiple origins possible?

[<gre...@un...>]

Hi Jon,

I don't know if this is possible, but Warren posted some weeks ago two
scripts you can run on two PyMOL sessions, in order to synchronize the =
view
on both visualization windows.
Have a look at these two links:
http://sourceforge.net/mailarchive/message.php?msg_id=3D14392630
and
http://sourceforge.net/mailarchive/message.php?msg_id=3D14394927

It might do the trick for you.

Cheers,

Greg


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Jon =
Manning
Sent: vendredi, 17. f=E9vrier 2006 19:59
To: pym...@li...
Subject: [PyMOL] Multiple origins possible?

Hi all,

I'm new new to PyMol, but have a question so would appreciate any=20
pointers people have. I currently read in a molecule to pymol, 'copy'=20
it, and color the two copies at different positions. I set a single=20
origin, being the centre of gravity of the combined molecules. Ideally,=20
I'd like to be able to set two origins, and have the molecules rotate=20
synchronously side-by-side rather than as one object, so I can compare=20
more easily. Is this possible with PyMol?

Thanks,

Jon

--=20

Smart Bomb: "Cogito Ergo Boom."


###########

Jonathan Manning
PhD Student
Barton Group
School of Life Sciences
University of Dundee
Scotland, UK
Tel +44 1382 388707

Re: [PyMOL] Multiple origins possible?

[Tsjerk W. <ts...@gm...>]

Hi Jon,

It is also possible to use the origin command to set the origin to a
specified position or to use a selection for determining the origin (origin
selection). In that way you can get what you want by setting the origin for
each molecule before doing a rotation.

Cheers,

Tsjerk

On 2/20/06, Gr=E9gori Gerebtzoff <gre...@un...> wrote:
>
> Hi Jon,
>
> I don't know if this is possible, but Warren posted some weeks ago two
> scripts you can run on two PyMOL sessions, in order to synchronize the
> view
> on both visualization windows.
> Have a look at these two links:
> http://sourceforge.net/mailarchive/message.php?msg_id=3D14392630
> and
> http://sourceforge.net/mailarchive/message.php?msg_id=3D14394927
>
> It might do the trick for you.
>
> Cheers,
>
> Greg
>
>
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Jon Manning
> Sent: vendredi, 17. f=E9vrier 2006 19:59
> To: pym...@li...
> Subject: [PyMOL] Multiple origins possible?
>
> Hi all,
>
> I'm new new to PyMol, but have a question so would appreciate any
> pointers people have. I currently read in a molecule to pymol, 'copy'
> it, and color the two copies at different positions. I set a single
> origin, being the centre of gravity of the combined molecules. Ideally,
> I'd like to be able to set two origins, and have the molecules rotate
> synchronously side-by-side rather than as one object, so I can compare
> more easily. Is this possible with PyMol?
>
> Thanks,
>
> Jon
>
> --
>
> Smart Bomb: "Cogito Ergo Boom."
>
>
> ###########
>
> Jonathan Manning
> PhD Student
> Barton Group
> School of Life Sciences
> University of Dundee
> Scotland, UK
> Tel +44 1382 388707
>
>
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

RE: [PyMOL] Multiple origins possible?

[Michael G. L. <ml...@um...>]

I was going to suggest the same thing.

FWIW, I have a version that you can run from your .pymolrc on my webpage=20
here:

http://www-personal.umich.edu/~mlerner/PyMOL/mg_pymol_utils.py

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

On Mon, 20 Feb 2006, Gr=E9gori Gerebtzoff wrote:

> Hi Jon,
>
> I don't know if this is possible, but Warren posted some weeks ago two
> scripts you can run on two PyMOL sessions, in order to synchronize the vi=
ew
> on both visualization windows.
> Have a look at these two links:
> http://sourceforge.net/mailarchive/message.php?msg_id=3D14392630
> and
> http://sourceforge.net/mailarchive/message.php?msg_id=3D14394927
>
> It might do the trick for you.
>
> Cheers,
>
> Greg
>
>
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Jon Manning
> Sent: vendredi, 17. f=E9vrier 2006 19:59
> To: pym...@li...
> Subject: [PyMOL] Multiple origins possible?
>
> Hi all,
>
> I'm new new to PyMol, but have a question so would appreciate any
> pointers people have. I currently read in a molecule to pymol, 'copy'
> it, and color the two copies at different positions. I set a single
> origin, being the centre of gravity of the combined molecules. Ideally,
> I'd like to be able to set two origins, and have the molecules rotate
> synchronously side-by-side rather than as one object, so I can compare
> more easily. Is this possible with PyMol?
>
> Thanks,
>
> Jon
>
> --=20
>
> Smart Bomb: "Cogito Ergo Boom."
>
>
> ###########
>
> Jonathan Manning
> PhD Student
> Barton Group
> School of Life Sciences
> University of Dundee
> Scotland, UK
> Tel +44 1382 388707
>
>
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log fi=
les
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>