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 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. (no subject) (Du, Sean) 2. Re: (no subject) (Elaine Meng) 3. Re: (no subject) (Eric Pettersen) 4. Re: Issue with surface modelling using Chimera (Elaine Meng) 5. saving a rotated map (Scott Stagg) 6. Re: saving a rotated map (Gabriel Lander) ---------------------------------------------------------------------- Message: 1 Date: Thu, 5 Mar 2009 14:08:39 -0800 From: "Du, Sean" <Sean.Du@maxygen.com> Subject: [Chimera-users] (no subject) To: <chimera-users@cgl.ucsf.edu> Message-ID: <3A581C9EE7D7DF43ACE4FAA43592FAEC07B3542B@rc-ga-mail-1.mxygn.com> Content-Type: text/plain; charset="us-ascii" Dear Chimera developers and sophisticated users, I have trouble to show the surfaces of serveral crystal structures, including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I would get pop-up error window and the following message in my Reply Log: C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 Since I don't have problem with other pdb files, such as 3dnn, I wonder if this problem is simply associated with some particular pdb files? If anyone out there knows a few tricks to overcome this, I'd really appreciate it. Many thanks in advance, Sean ---------------------------------------------- Sean Du, Ph.D. Senior Scientist, Project Leader Maxygen, Inc. 515 Galveston Drive Redwood City, CA 94063 Office: (650) 298-5380 Cell: (510) 366-3586 -----------------------------------------------
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