commands to add red spheres to the ribbon structure
Hi Chimera, I would like to know the commands for adding a red sphere to a certain spot in a ribbon structure of a protein (please see the attachment). The command I know worked for older version of the chimera but not this new version 0.1. Thanks, Bin
Hi Bin, As far as I know, the same commands as in earlier versions should work. However, the trick (same as before) is to use the “ribbackbone” command to allow showing backbone atoms at the same time as ribbon. Then you can show the alpha-carbon as a red ball. For example, commands: open 1hd2 ribbackbone # hide atoms ~disp disp :57@ca repr sphere :57@ca color red,a :57@ca In the last command, “,a” means atoms-only (not ribbon etc.). I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2017, at 10:00 AM, zhangbin <mumu730@gmail.com> wrote:
Hi Chimera, I would like to know the commands for adding a red sphere to a certain spot in a ribbon structure of a protein (please see the attachment). The command I know worked for older version of the chimera but not this new version 0.1.
Thanks, Bin
Hi Bin, I assumed you were using Chimera. If you are using ChimeraX, that’s a different story. Then after opening the structure it would be something like cartoon suppress false hide show :57@ca style :57@ca sphere color :57@ca red target a If you’re using ChimeraX, make sure to say so if you e-mail questions to this list in the future. Also, there is a separate list you could use instead: chimerax-users@cgl.ucsf.edu “cartoon suppress false” in ChimeraX is similar to Chimera’s “ribbackbone" Best, Elaine
On Jul 17, 2017, at 12:52 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Bin, As far as I know, the same commands as in earlier versions should work. However, the trick (same as before) is to use the “ribbackbone” command to allow showing backbone atoms at the same time as ribbon. Then you can show the alpha-carbon as a red ball. For example, commands:
open 1hd2 ribbackbone # hide atoms ~disp disp :57@ca repr sphere :57@ca color red,a :57@ca
In the last command, “,a” means atoms-only (not ribbon etc.). I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2017, at 10:00 AM, zhangbin <mumu730@gmail.com> wrote:
Hi Chimera, I would like to know the commands for adding a red sphere to a certain spot in a ribbon structure of a protein (please see the attachment). The command I know worked for older version of the chimera but not this new version 0.1.
Thanks, Bin
If you were using the shape command in Chimera, then you need to keep using Chimera, because the shape command is not in ChimeraX yet. -- Greg On 07/17/2017 01:11 PM, Elaine Meng wrote:
Hi Bin, I assumed you were using Chimera. If you are using ChimeraX, that’s a different story. Then after opening the structure it would be something like
cartoon suppress false hide show :57@ca style :57@ca sphere color :57@ca red target a
If you’re using ChimeraX, make sure to say so if you e-mail questions to this list in the future. Also, there is a separate list you could use instead: chimerax-users@cgl.ucsf.edu
“cartoon suppress false” in ChimeraX is similar to Chimera’s “ribbackbone"
Best, Elaine
On Jul 17, 2017, at 12:52 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Bin, As far as I know, the same commands as in earlier versions should work. However, the trick (same as before) is to use the “ribbackbone” command to allow showing backbone atoms at the same time as ribbon. Then you can show the alpha-carbon as a red ball. For example, commands:
open 1hd2 ribbackbone # hide atoms ~disp disp :57@ca repr sphere :57@ca color red,a :57@ca
In the last command, “,a” means atoms-only (not ribbon etc.). I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2017, at 10:00 AM, zhangbin <mumu730@gmail.com> wrote:
Hi Chimera, I would like to know the commands for adding a red sphere to a certain spot in a ribbon structure of a protein (please see the attachment). The command I know worked for older version of the chimera but not this new version 0.1.
Thanks, Bin
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Oh yes forgot to mention I was using ChimeraX! Thank you so much! Bin Sent from my iPhone
On Jul 17, 2017, at 3:18 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
If you were using the shape command in Chimera, then you need to keep using Chimera, because the shape command is not in ChimeraX yet.
-- Greg
On 07/17/2017 01:11 PM, Elaine Meng wrote: Hi Bin, I assumed you were using Chimera. If you are using ChimeraX, that’s a different story. Then after opening the structure it would be something like
cartoon suppress false hide show :57@ca style :57@ca sphere color :57@ca red target a
If you’re using ChimeraX, make sure to say so if you e-mail questions to this list in the future. Also, there is a separate list you could use instead: chimerax-users@cgl.ucsf.edu
“cartoon suppress false” in ChimeraX is similar to Chimera’s “ribbackbone"
Best, Elaine
On Jul 17, 2017, at 12:52 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Bin, As far as I know, the same commands as in earlier versions should work. However, the trick (same as before) is to use the “ribbackbone” command to allow showing backbone atoms at the same time as ribbon. Then you can show the alpha-carbon as a red ball. For example, commands:
open 1hd2 ribbackbone # hide atoms ~disp disp :57@ca repr sphere :57@ca color red,a :57@ca
In the last command, “,a” means atoms-only (not ribbon etc.). I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2017, at 10:00 AM, zhangbin <mumu730@gmail.com> wrote:
Hi Chimera, I would like to know the commands for adding a red sphere to a certain spot in a ribbon structure of a protein (please see the attachment). The command I know worked for older version of the chimera but not this new version 0.1.
Thanks, Bin
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
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Elaine Meng -
Greg Couch -
mumu730 -
zhangbin