Hi,
I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much.
Best,
Stephen
Hi Stephen, I'm not sure what you mean by "didn't work" but I'm guessing you are showing a ribbon. By default, if ribbon is shown you cannot also show CA atoms for the same residues at the same time until after you enter the command "ribbackbone" (show the command line first with menu: Favorites... Command Line). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html
Then you can display whichever CA atoms you like at the same time as the ribbon, for example, command:
display :50.A@CA
... to show CA atom of residue 50 in chain A.
Since the default ribbon is a smoothed interpolated path, another issue is that the CA atoms may not be on the ribbon but "floating" in space nearby. Possible ways to handle this issue:
(1) show the CA atoms as fairly large balls so that it is less obvious that they are not on the ribbon. Maybe you are showing "balls" (default 0.25 of VDW radius) and could instead show "spheres" (equal to VDW radius). You can also change VDW radius with the command "vdwdefine". For example to show CAs as balls and increase their VDW radii by 1.0:
repr bs @ca vdwdefine +1.0 @ca
The atoms should be represented as balls or spheres (not stick) or else you won't see the difference in size.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html
(2) instead of showing ribbon, just show the CA atom trace as sticks and any specific CA atoms you want to highlight as balls or spheres. I agree this is not as pretty as the ribbon, however.
(3) instead of the default B-spline ribbon, instead use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands:
ribspline cardinal ribspline cardinal smooth strand
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html
These things can also be done with menus/GUIs but it would take a lot more typing to describe. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2013, at 1:46 PM, Xiongzhuo Gao wrote:
Hi, I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much. Best, Stephen
Hi Elaine,
Following your suggestion I can show the CA in the way that I want. Thank you so much for your help.
Best Wishes,
Stephen ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Tuesday, March 26, 2013 7:20 PM To: Xiongzhuo Gao Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] sphere representation for specific atoms
Hi Stephen, I'm not sure what you mean by "didn't work" but I'm guessing you are showing a ribbon. By default, if ribbon is shown you cannot also show CA atoms for the same residues at the same time until after you enter the command "ribbackbone" (show the command line first with menu: Favorites... Command Line). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html
Then you can display whichever CA atoms you like at the same time as the ribbon, for example, command:
display :50.A@CA
... to show CA atom of residue 50 in chain A.
Since the default ribbon is a smoothed interpolated path, another issue is that the CA atoms may not be on the ribbon but "floating" in space nearby. Possible ways to handle this issue:
(1) show the CA atoms as fairly large balls so that it is less obvious that they are not on the ribbon. Maybe you are showing "balls" (default 0.25 of VDW radius) and could instead show "spheres" (equal to VDW radius). You can also change VDW radius with the command "vdwdefine". For example to show CAs as balls and increase their VDW radii by 1.0:
repr bs @ca vdwdefine +1.0 @ca
The atoms should be represented as balls or spheres (not stick) or else you won't see the difference in size.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html
(2) instead of showing ribbon, just show the CA atom trace as sticks and any specific CA atoms you want to highlight as balls or spheres. I agree this is not as pretty as the ribbon, however.
(3) instead of the default B-spline ribbon, instead use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands:
ribspline cardinal ribspline cardinal smooth strand
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html
These things can also be done with menus/GUIs but it would take a lot more typing to describe. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2013, at 1:46 PM, Xiongzhuo Gao wrote:
Hi, I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much. Best, Stephen
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Elaine Meng -
Xiongzhuo Gao