[Chimera-users] Regarding backbone images for protein structures

Saurabh Gupte ssgupte at sfsu.edu
Wed Mar 17 14:57:55 PDT 2010

After hiding the ribbons, I am able to view the backbone atom structure.
Thanks everyone for the assistance.


On Mon, Mar 15, 2010 at 2:17 PM, Thomas Goddard <goddard at cgl.ucsf.edu>wrote:

> 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)
>        ~ribbon
> 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.
>        Tom
>  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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