Hello, I don't seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains. I can't figure out how to get an expression like "color green, chain C C" Or something like that ... How to go about this? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller@cdrd.ca<mailto:kessabar@cdrd.ca> | www.cdrd.ca
Hi Markus, How about Chimera commands color byelement ~color element.C The first line colors the carbons gray, and the second says to unset their color, which makes them default to the color set for each molecule. Tom On May 14, 2013, at 11:42 AM, Markus Heller <mheller@cdrd.ca> wrote:
Hello,
I don’t seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains.
I can’t figure out how to get an expression like
“color green, chain C C”
Or something like that …
How to go about this?
Thanks and Cheers Markus
-- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller@cdrd.ca | www.cdrd.ca
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, This works, thanks. Although it seems to be a bit of a roundabout way of going about this ... :-/ Cheers Markus From: Tom Goddard [mailto:goddard@sonic.net] Sent: Tuesday, May 14, 2013 12:11 PM To: Markus Heller Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Carbon color of 1 chain Hi Markus, How about Chimera commands color byelement ~color element.C The first line colors the carbons gray, and the second says to unset their color, which makes them default to the color set for each molecule. Tom On May 14, 2013, at 11:42 AM, Markus Heller <mheller@cdrd.ca<mailto:mheller@cdrd.ca>> wrote: Hello, I don't seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains. I can't figure out how to get an expression like "color green, chain C C" Or something like that ... How to go about this? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller@cdrd.ca<mailto:kessabar@cdrd.ca> | www.cdrd.ca<x-msg://116/www.cdrd.ca> _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
If you pick your own colors, you can use something like: color green C & :.D to color all carbons in chain D. "C" is an alias for all atoms (which you can actually see in the Select -> element menu :-). "&" is the intersect operator. ":.D" means all atoms in chain D. Conrad On 5/14/13 12:29 PM, Markus Heller wrote:
Hi Tom,
This works, thanks. Although it seems to be a bit of a roundabout way of going about this … :-/
Cheers
Markus
*From:*Tom Goddard [mailto:goddard@sonic.net] *Sent:* Tuesday, May 14, 2013 12:11 PM *To:* Markus Heller *Cc:* chimera-users@cgl.ucsf.edu *Subject:* Re: [Chimera-users] Carbon color of 1 chain
Hi Markus,
How about Chimera commands
color byelement
~color element.C
The first line colors the carbons gray, and the second says to unset their color, which makes them default to the color set for each molecule.
Tom
On May 14, 2013, at 11:42 AM, Markus Heller <mheller@cdrd.ca <mailto:mheller@cdrd.ca>> wrote:
Hello,
I don’t seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains.
I can’t figure out how to get an expression like
“color green, chain C C”
Or something like that …
How to go about this?
Thanks and Cheers
Markus
--
*Markus Heller, Ph.D.*
NMR Scientist
CDRD - The Centre for Drug Research and Development
2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147
Direct: (604) 827-1122| F: (604) 827-1299 | E:mheller@cdrd.ca <mailto:kessabar@cdrd.ca>|www.cdrd.ca <x-msg://116/www.cdrd.ca>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Uh. "C" is an alias for all atoms -> "C" is an alias for all carbon atoms oops. Conrad On 5/14/13 12:36 PM, Conrad Huang wrote:
If you pick your own colors, you can use something like:
color green C & :.D
to color all carbons in chain D. "C" is an alias for all atoms (which you can actually see in the Select -> element menu :-). "&" is the intersect operator. ":.D" means all atoms in chain D.
Conrad
On 5/14/13 12:29 PM, Markus Heller wrote:
Hi Tom,
This works, thanks. Although it seems to be a bit of a roundabout way of going about this … :-/
Cheers
Markus
*From:*Tom Goddard [mailto:goddard@sonic.net] *Sent:* Tuesday, May 14, 2013 12:11 PM *To:* Markus Heller *Cc:* chimera-users@cgl.ucsf.edu *Subject:* Re: [Chimera-users] Carbon color of 1 chain
Hi Markus,
How about Chimera commands
color byelement
~color element.C
The first line colors the carbons gray, and the second says to unset their color, which makes them default to the color set for each molecule.
Tom
On May 14, 2013, at 11:42 AM, Markus Heller <mheller@cdrd.ca <mailto:mheller@cdrd.ca>> wrote:
Hello,
I don’t seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains.
I can’t figure out how to get an expression like
“color green, chain C C”
Or something like that …
How to go about this?
Thanks and Cheers
Markus
--
*Markus Heller, Ph.D.*
NMR Scientist
CDRD - The Centre for Drug Research and Development
2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147
Direct: (604) 827-1122| F: (604) 827-1299 | E:mheller@cdrd.ca <mailto:kessabar@cdrd.ca>|www.cdrd.ca <x-msg://116/www.cdrd.ca>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Conrad, Just what I was looking for! Thanks a lot! Markus -----Original Message----- From: Conrad Huang [mailto:conrad@cgl.ucsf.edu] Sent: Tuesday, May 14, 2013 12:39 PM To: Markus Heller Cc: chimera-users@cgl.ucsf.edu; Tom Goddard Subject: Re: [Chimera-users] Carbon color of 1 chain Uh. "C" is an alias for all atoms -> "C" is an alias for all carbon atoms oops. Conrad On 5/14/13 12:36 PM, Conrad Huang wrote:
If you pick your own colors, you can use something like:
color green C & :.D
to color all carbons in chain D. "C" is an alias for all atoms (which you can actually see in the Select -> element menu :-). "&" is the intersect operator. ":.D" means all atoms in chain D.
Conrad
On 5/14/13 12:29 PM, Markus Heller wrote:
Hi Tom,
This works, thanks. Although it seems to be a bit of a roundabout way of going about this ... :-/
Cheers
Markus
*From:*Tom Goddard [mailto:goddard@sonic.net] *Sent:* Tuesday, May 14, 2013 12:11 PM *To:* Markus Heller *Cc:* chimera-users@cgl.ucsf.edu *Subject:* Re: [Chimera-users] Carbon color of 1 chain
Hi Markus,
How about Chimera commands
color byelement
~color element.C
The first line colors the carbons gray, and the second says to unset their color, which makes them default to the color set for each molecule.
Tom
On May 14, 2013, at 11:42 AM, Markus Heller <mheller@cdrd.ca <mailto:mheller@cdrd.ca>> wrote:
Hello,
I don't seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains.
I can't figure out how to get an expression like
"color green, chain C C"
Or something like that ...
How to go about this?
Thanks and Cheers
Markus
--
*Markus Heller, Ph.D.*
NMR Scientist
CDRD - The Centre for Drug Research and Development
2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147
Direct: (604) 827-1122| F: (604) 827-1299 | E:mheller@cdrd.ca <mailto:kessabar@cdrd.ca>|www.cdrd.ca <x-msg://116/www.cdrd.ca>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Note the following command will color all atoms except carbon by element. The carbons will remain whatever color they were previously. color byhet There are usually several ways to do any given thing! Elaine On May 14, 2013, at 12:41 PM, Markus Heller <mheller@cdrd.ca> wrote:
Conrad,
Just what I was looking for!
Thanks a lot!
Markus
-----Original Message----- From: Conrad Huang [mailto:conrad@cgl.ucsf.edu] Sent: Tuesday, May 14, 2013 12:39 PM To: Markus Heller Cc: chimera-users@cgl.ucsf.edu; Tom Goddard Subject: Re: [Chimera-users] Carbon color of 1 chain
Uh.
"C" is an alias for all atoms -> "C" is an alias for all carbon atoms
oops.
Conrad
On 5/14/13 12:36 PM, Conrad Huang wrote:
If you pick your own colors, you can use something like:
color green C & :.D
to color all carbons in chain D. "C" is an alias for all atoms (which you can actually see in the Select -> element menu :-). "&" is the intersect operator. ":.D" means all atoms in chain D.
Conrad
On 5/14/13 12:29 PM, Markus Heller wrote:
Hi Tom,
This works, thanks. Although it seems to be a bit of a roundabout way of going about this ... :-/
Cheers
Markus
*From:*Tom Goddard [mailto:goddard@sonic.net] *Sent:* Tuesday, May 14, 2013 12:11 PM *To:* Markus Heller *Cc:* chimera-users@cgl.ucsf.edu *Subject:* Re: [Chimera-users] Carbon color of 1 chain
Hi Markus,
How about Chimera commands
color byelement
~color element.C
The first line colors the carbons gray, and the second says to unset their color, which makes them default to the color set for each molecule.
Tom
On May 14, 2013, at 11:42 AM, Markus Heller <mheller@cdrd.ca <mailto:mheller@cdrd.ca>> wrote:
Hello,
I don't seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains.
I can't figure out how to get an expression like
"color green, chain C C"
Or something like that ...
How to go about this?
Thanks and Cheers
Markus
--
*Markus Heller, Ph.D.*
NMR Scientist
CDRD - The Centre for Drug Research and Development
2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147
Direct: (604) 827-1122| F: (604) 827-1299 | E:mheller@cdrd.ca <mailto:kessabar@cdrd.ca>|www.cdrd.ca <x-msg://116/www.cdrd.ca>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Markus, There are always multiple ways to do things in Chimera. Here's a one-liner if you prefer color byelement ~element.C The "~" in front of element.C means "not". Tom On May 14, 2013, at 12:29 PM, Markus Heller wrote:
Hi Tom,
This works, thanks. Although it seems to be a bit of a roundabout way of going about this … :-/
Cheers Markus
From: Tom Goddard Sent: Tuesday, May 14, 2013 12:11 PM To: Markus Heller Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Carbon color of 1 chain
Hi Markus,
How about Chimera commands
color byelement ~color element.C
The first line colors the carbons gray, and the second says to unset their color, which makes them default to the color set for each molecule.
Tom
On May 14, 2013, at 11:42 AM, Markus Heller <mheller@cdrd.ca> wrote:
Hello,
I don’t seem to be able to figure out how to color a scene by element, but with different carbon colors for different chains.
I can’t figure out how to get an expression like
“color green, chain C C”
Or something like that …
How to go about this?
Thanks and Cheers Markus
-- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller@cdrd.ca | www.cdrd.ca
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Conrad Huang -
Elaine Meng -
Markus Heller -
Tom Goddard