[Chimera-users] Regarding backbone images for protein structures

Thomas Goddard goddard at cgl.ucsf.edu
Mon Mar 15 14:17:42 PDT 2010

Hi Saurabh,

   It is a bit weird but Chimera can display both a ribbon and the 
backbone atoms, but the ribbon would hide the view of the backbone 
atoms.  So "show minimal" still works to show the backbone atoms but you 
would also need to undisplay the ribbon (command starts with tilde)


to be able to see the backbone atoms.  As Elaine points out you can set 
a preference so Chimera 1.4 won't show the ribbon by default.


> Hello Saurabh,
> Starting with Chimera 1.4 the default initial display of a molecule is
> nicer: ribbons instead of all atoms. However, you can get all atoms
> shown initially if that is what you prefer. If you want that all the
> time, just change your preferences (Favorites... Preferences, go to "New
> Molecules" category, set "smart initial display" to false, click Save).
> If you just want it sometimes and you are using the "open" command
> inside of Chimera, use "open noprefs." Or, just hide the ribbon after
> you open the structure if that is what is bothering you, or use the all
> atoms Preset.
> This is not a bug. This change and how to circumvent it (as included
> above) are described in the 1.4 release notes,
> <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Mar 14, 2010, at 10:41 PM, Saurabh Gupte wrote:
>> Hello,
>> I have been using Chimera for observing the 3D model of protein
>> structures. For viewing the backbone structure, I used the following
>> commands:
>> show backbone or show minimal
>> But in the latest production version 1.4, I am not able to view the
>> backbone/minimal structure. The 3D structure is rendered properly but
>> the above command do not seem to work. Have there been any changes in
>> the format for above commands or have they been substituted by some
>> other commands?
>> Thanks,
>> Saurabh

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