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
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 stephane.a...@cea.fr 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
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 stephane.a...@cea.fr 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
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 stephane.a...@cea.fr 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
