Re: [PyMOL] Create a dummy atom
Hi Troels,
> I think to get the return values of a script, you need to put them
> inside python boxes
I'd assume it'd be a Python script :) But also for a PyMOL script,
it's not exactly true. However, then there should be no space before
the equality sign. This should work:
theCenter=COM(...)
pseudoatom("theAtom",pos=theCenter)
Groetjes,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
RSA(R) Conference 2012
Save $700 by Nov 18
Register now
http://p.sf.net/sfu/rsa-sfdev2dev1
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Create a dummy atom
I think to get the return values of a script, you need to put them
inside python boxes
python
theCenter = COM(...)
pseudoatom("theAtom",pos=theCenter)
python end
2011/11/14 ABEL Stephane 175950
> Thank you Jason and Troels for your quick response.
>
> I have an additional question. Now if i want to pass the COM coordinates
> x, y and z obtained with the COM script in the pseudoatom pos. For example
> to use in the script
>
> How i can do that ?
>
> Thank you again for your response.
>
> Stephane
>
> --
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
RSA(R) Conference 2012
Save $700 by Nov 18
Register now
http://p.sf.net/sfu/rsa-sfdev2dev1___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Create a dummy atom
Stephane, COM should return the coordinates: theCenter = COM(...) pseudoatom theAtom, pos=theCenter Cheers, -- Jason On Mon, Nov 14, 2011 at 5:44 PM, ABEL Stephane 175950 wrote: > Thank you Jason and Troels for your quick response. > > I have an additional question. Now if i want to pass the COM coordinates x, y > and z obtained with the COM script in the pseudoatom pos. For example to use > in the script > > How i can do that ? > > Thank you again for your response. > > Stephane > -- > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Create a dummy atom
Thank you Jason and Troels for your quick response. I have an additional question. Now if i want to pass the COM coordinates x, y and z obtained with the COM script in the pseudoatom pos. For example to use in the script How i can do that ? Thank you again for your response. Stephane -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Create a dummy atom
Stephane, Create a psuedoatom and specify the coordinates: pseudoatom myCentralAtom, pos=[X,Y,Z] pseudoatom myCentralAtom, pos=[10.20, -14.2, 0.44] Cheers, -- Jason On Mon, Nov 14, 2011 at 4:33 PM, ABEL Stephane 175950 wrote: > Dear all, > > I have a simple question but i have found no response: i have downloaded a > pymol script COM.py from the pymol wiki to obtain the coordinates x, y and z > of the center of mass of my protein. Now i would like to create a dummy at > these coordinates. How to do that with pymol ? > > Thank for your help > > Stephane > -- > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Create a dummy atom
Using pseudo atoms http://www.pymolwiki.org/index.php/Pseudoatom using pos= pseudoatom tmpPoint2, resi=40, chain=ZZ, b=40, color=tv_blue, pos=[-10, 0, 10] Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 2011/11/14 ABEL Stephane 175950 > Dear all, > > I have a simple question but i have found no response: i have downloaded a > pymol script COM.py from the pymol wiki to obtain the coordinates x, y and > z of the center of mass of my protein. Now i would like to create a dummy > at these coordinates. How to do that with pymol ? > > Thank for your help > > Stephane > > -- > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Create a dummy atom
Dear all, I have a simple question but i have found no response: i have downloaded a pymol script COM.py from the pymol wiki to obtain the coordinates x, y and z of the center of mass of my protein. Now i would like to create a dummy at these coordinates. How to do that with pymol ? Thank for your help Stephane -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
