Gap between C=O mainchain bond and supersmooth ribbon
Dear all,
I want to represent the C=O bond that chelates an ion in my structure and
the rest of the prot in ribbon (supersmooth). I don't want the carbon
explicitly represented but yes the bond and the oxygen with a ball and stick
representation. Following a previous post, I have two copies of my model.
One is represented in ribbon. In the other one, I have the oxygen in bs and
for the bond I did "bonddisplay always #1:22@C,O". It does pretty much what
I want but I see that in many cases I have a empty gap between the end of
the bond and the ribbon. Something I don't want. Is there a way to remove
this gap? Or should I always represent the carbon also (something I find
less esthetic that the other option).
All the best,
JD
-----Mensaje original-----
De: chimera-users-bounces@cgl.ucsf.edu
[mailto:chimera-users-bounces@cgl.ucsf.edu] En nombre de
chimera-users-request@cgl.ucsf.edu
Enviado el: viernes, 06 de marzo de 2009 5:16
Para: chimera-users@cgl.ucsf.edu
Asunto: Chimera-users Digest, Vol 71, Issue 6
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----------------------------------------------------------------------
Message: 1
Date: Thu, 5 Mar 2009 14:08:39 -0800
From: "Du, Sean"
Hi JD, The path of the ribbon is a smoothed interpolation over the backbone atom locations, so regardless of style (smooth, supersmooth, edged, flat, etc.) the "real" backbone atom positions do not necessarily fall on the ribbon. Showing both the ribbon and backbone atoms can be enabled with the command "ribbackbone". However, even if the atoms are shown you will still have the same gap as when you displayed just the bond. Currently there is no way to get rid of gaps between ribbon and any displayed backbone atoms. We would like to allow constraining the ribbon to go closer to the actual atom positions, but this has not been done yet. It is problem report #6661: http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/6661 This common problem is discussed in previous posts: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002385.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003295.html
I will attempt to put you on the notification list for changes to the problem report #6661. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 6, 2009, at 2:41 AM, Dr. Jean-Didier Maréchal wrote:
Dear all,
I want to represent the C=O bond that chelates an ion in my structure and the rest of the prot in ribbon (supersmooth). I don't want the carbon explicitly represented but yes the bond and the oxygen with a ball and stick representation. Following a previous post, I have two copies of my model. One is represented in ribbon. In the other one, I have the oxygen in bs and for the bond I did "bonddisplay always #1:22@C,O". It does pretty much what I want but I see that in many cases I have a empty gap between the end of the bond and the ribbon. Something I don't want. Is there a way to remove this gap? Or should I always represent the carbon also (something I find less esthetic that the other option).
All the best, JD
participants (2)
-
Dr. Jean-Didier Maréchal -
Elaine Meng