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 -----------------------------------------------