Re: [PyMOL] cartoon_sidechain_helper
Strange, yesterday I did a quick test and it didn't work. But here on my main machine everything is fine. Sorry for the noice. jsutin On 13/11/11 17:48, Jason Vertrees wrote: Hi Justin, It works; see http://www.pymolwiki.org/index.php/File:Cartoon_side_chain_helper_on.png. You just have to color by atom type after coloring by secondary structure: set cartoon_sidechain_helper, on C Color by ss Helix (red) Sheet (yellow) Loop (green) C Color by element ... Cheers, -- Jason On Sun, Nov 13, 2011 at 7:11 AM, Justin Lecher j.lec...@fz-juelich.de wrote: Hi, while trying this http://kpwu.wordpress.com/2011/11/12/pymol-sidechain-helper-in-the-cartoon-view/ I recognised that the color by atom type function doesn't work anymore if the sidechain helper is on. Bug or feature? Could we enable it? Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- 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 -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- 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
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
[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, 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
