Re: [PyMOL] color by element
What I personally do is: cmd.color(grey50,all) util.cnc(all) So that my carbons have the color I wish (grey50), and other atoms are colored by element. Best, Greg -Original Message- From: David Hall [mailto:li...@cowsandmilk.net] Sent: Wednesday, February 10, 2010 1:45 AM To: Ariel Talavera Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] color by element First of all, there is: color atomic which will do all the colors and for whatever reason does green for carbons Additionally, there's a general class of util.cba? where question mark is replaced by one letter representing the color of carbon. I've been told by people that these are supposed to be internal commands and I shouldn't use them, but I do and they've been there as long as I've used pymol. Currently, these are: util.cbab for slate util.cbag for green util.cbam for magenta util.cbap for purple util.cbaw for white util.cbac for cyan util.cbak for pink util.cbao for orange util.cbas for salmon util.cbay for yellow You can see how these are implemented in http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/modules/pymol/util.py?view=markup if you want to make your own custom versions. -David Hall On Tue, Feb 9, 2010 at 5:46 PM, Ariel Talavera talav...@cim.sld.cu wrote: Hi Pymolers, How can I use the color by element (HNOS) function present in the GUI, in a script? Thanks in advanced, Best, Ariel -- * Ariel Talavera Pérez, PhD Center of Molecular Immunology calle 216 esq. A 15, Atabey, Playa Havana 11600, CUBA tel: (53-7) 271 7933, ext. 221 fax: (53-7) 272 0644 email: talav...@cim.sld.cu * -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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] color by element
On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera talav...@cim.sld.cu wrote: How can I use the color by element (HNOS) function present in the GUI, in a script? I don't think there's a single command that does this; I've always done something like this: color grey80, elem c color white, elem h color red, elem o color blue, elem n color orange, elem s and so on (in python, these become 'cmd.color(grey80, elem c)', etc.). I just discovered that there is also a separate color name for each element, e.g. color carbon, elem c will work, but the default coloring scheme seems a bit wacky sometimes (carbon is green, etc.). If there was a convenient way to switch between available color sets (e.g. all of the options available in the menus), that would be awesome. Currently the atom-name colors are hardcoded in C, unfortunately. Nat -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ 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] color by element
have you tried: import util util.cbag util.cbay util.rainbow etc? after you type import util, you can type util. followed by a tab to see the available commands. On Tue, Feb 9, 2010 at 6:09 PM, Nathaniel Echols nathaniel.ech...@gmail.com wrote: On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera talav...@cim.sld.cuwrote: How can I use the color by element (HNOS) function present in the GUI, in a script? I don't think there's a single command that does this; I've always done something like this: color grey80, elem c color white, elem h color red, elem o color blue, elem n color orange, elem s and so on (in python, these become 'cmd.color(grey80, elem c)', etc.). I just discovered that there is also a separate color name for each element, e.g. color carbon, elem c will work, but the default coloring scheme seems a bit wacky sometimes (carbon is green, etc.). If there was a convenient way to switch between available color sets (e.g. all of the options available in the menus), that would be awesome. Currently the atom-name colors are hardcoded in C, unfortunately. Nat -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ 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] color by element
First of all, there is: color atomic which will do all the colors and for whatever reason does green for carbons Additionally, there's a general class of util.cba? where question mark is replaced by one letter representing the color of carbon. I've been told by people that these are supposed to be internal commands and I shouldn't use them, but I do and they've been there as long as I've used pymol. Currently, these are: util.cbab for slate util.cbag for green util.cbam for magenta util.cbap for purple util.cbaw for white util.cbac for cyan util.cbak for pink util.cbao for orange util.cbas for salmon util.cbay for yellow You can see how these are implemented in http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/modules/pymol/util.py?view=markup if you want to make your own custom versions. -David Hall On Tue, Feb 9, 2010 at 5:46 PM, Ariel Talavera talav...@cim.sld.cu wrote: Hi Pymolers, How can I use the color by element (HNOS) function present in the GUI, in a script? Thanks in advanced, Best, Ariel -- * Ariel Talavera Pérez, PhD Center of Molecular Immunology calle 216 esq. A 15, Atabey, Playa Havana 11600, CUBA tel: (53-7) 271 7933, ext. 221 fax: (53-7) 272 0644 email: talav...@cim.sld.cu * -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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
