[Chimera-users] Fwd: longbond and session restore problems

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 14 11:06:26 PST 2006

Begin forwarded message:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Date: November 14, 2006 10:36:35 AM PST
> To: jean-francois menetret <menetret at bu.edu>
> Cc: Eric Pettersen <pett at cgl.ucsf.edu>, Thomas Goddard  
> <goddard at cgl.ucsf.edu>, Elaine Meng <meng at 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 at bu.edu
>> Mailing address: 715 Albany Street
> -----
> Elaine C. Meng, Ph.D.                          meng at 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

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