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 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
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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 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
have you tried:
import util
util.cbag
util.cbay
util.rainbow
etc?
after you type "import util", you can type "util." followed by a to
see the available commands.
On Tue, Feb 9, 2010 at 6:09 PM, Nathaniel Echols wrote:
> On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera 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
>
--
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)
--
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Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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Re: [PyMOL] color by element
On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera 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
[PyMOL] color by element
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
