help with chimerax wildcards
Hi, I am trying to use wild cards in chimerax but they appear not to work. I type the command
color @N* blue
and get as response Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
All I am trying to do is color all nitrogens blue. Version 0.5 (2018-02-05) running on macOS Sierra v10.12.6
what am I doing wrong?
thanks
Mike Lawrence
Hi Mike, Are you sure you didn’t use Chimera syntax, which has the color before the spec? That is the common reason for this error.
Your command looks fine, and works for me when I try it in daily build (2/19) and 0.8 release (12/17/2018).
However, the simpler approach for element N is just to use element symbol:
color N blue
Also if you don’t want to also color the ribbons entirely blue (all amino acids have N), you may want to add that target is atoms:
color N blue target a - or - color N blue atoms
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 17, 2019, at 1:17 PM, Michael Lawrence mikeclawrence@gmail.com wrote:
Hi, I am trying to use wild cards in chimerax but they appear not to work. I type the command
color @N* blue
and get as response Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
All I am trying to do is color all nitrogens blue. Version 0.5 (2018-02-05) running on macOS Sierra v10.12.6
what am I doing wrong?
thanks
Mike Lawrence
Hi Elaine, thanks for your help - yes, the problem disappears when I use the latest build. Sincerely Mike
On Wed, 20 Feb 2019, 04:06 Elaine Meng <meng@cgl.ucsf.edu wrote:
Hi Mike, Are you sure you didn’t use Chimera syntax, which has the color before the spec? That is the common reason for this error.
Your command looks fine, and works for me when I try it in daily build (2/19) and 0.8 release (12/17/2018).
However, the simpler approach for element N is just to use element symbol:
color N blue
Also if you don’t want to also color the ribbons entirely blue (all amino acids have N), you may want to add that target is atoms:
color N blue target a
- or -
color N blue atoms
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 17, 2019, at 1:17 PM, Michael Lawrence mikeclawrence@gmail.com
wrote:
Hi, I am trying to use wild cards in chimerax but they appear not to
work. I type the command
color @N* blue
and get as response Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
All I am trying to do is color all nitrogens blue. Version 0.5 (2018-02-05) running on macOS Sierra v10.12.6
what am I doing wrong?
thanks
Mike Lawrence
participants (2)
-
Elaine Meng
-
Michael Lawrence