Begin forwarded message:
From: Elaine Meng <meng@cgl.ucsf.edu> Date: November 14, 2006 10:36:35 AM PST To: jean-francois menetret <menetret@bu.edu> Cc: Eric Pettersen <pett@cgl.ucsf.edu>, Thomas Goddard <goddard@cgl.ucsf.edu>, Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] longbond and session restore problems
Hi Jean-Francois, In my tests I didn't have this problem; showing Pipes-and-Planks should not change which atoms and bonds are shown.
However, I might understand what is happening: when you show the "chain trace" of CA atoms only, a connection across the missing part is shown even after you use "~longbond". This CA connection line is different than the "missing segments" pseudobonds:
-CA-CA-------CA-CA- is the chain trace, not affected by ~longbond
-N-CA-C- - - -N-CA-C- is the backbone showing "real bonds" except for the pseudobond, which is affected by ~longbond
If you are showing just the CA atoms and you don't want the connection, here are some possibilities: (1) just hide all the CA atoms (for example, command: ~disp @ca) OR (2) change from "chain trace" (the CA atoms) to "backbone only" (N,CA,C) - if you used ~longbond the connection will be gone OR (3) if you really wanted to keep showing just the CA atoms, you can select each long CA-CA bond (which is also a pseudobond, although not shown with a dashed line) with Ctrl-click, and use the Selection Inspector to undisplay it. This tool is opened by clicking the button on the lower right of the Chimera window. In the Inspector, change to Inspect [Pseudobond] and change the "displayed" attribute to "false."
I hope this helps, Elaine
On Nov 14, 2006, at 6:51 AM, jean-francois menetret wrote:
Hi Elaine,
thank you for your message I still have one problem with the long bonds, though : there reappear in pipes-and-plancks. About restoring a session, I agree, it was not an issue with the chimera version but with the speed/memory of my PC. Although chimera could save the session, it couldn't reopen it on my PC but it did on a faster one.
Best wishes
Jean-François Ménétret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret@bu.edu Mailing address: 715 Albany Street
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html