[Chimera-users] show alpha-carbon as sphere in chimera

Feixia fvy2 at unh.edu
Tue Mar 19 17:30:31 PDT 2013


Yes, very helpful!  Thank you so much!

Best,
Feixia

On Tue, 19 Mar 2013 12:29:18 -0400, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> On Mar 18, 2013, at 8:07 PM, Feixia wrote:
>
>> Hi Elaine,
>> Is there a way to show alpha-carbon only in Chimera as sphere?  I can  
>> show beta-carbon, but always together with alpha-carbon.  Alpha-carbon  
>> for some reason doesn't show by itself.  Thanks a lot.
>> Best,
>> Feixia
>
> Hi Feixia,
> Maybe you are also displaying ribbon.  By default when the ribbon is  
> shown, the alpha-carbon will not show.  You can allow showing both  
> ribbon and alpha-carbon with command:
> ribbackbone
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>
>
> However, you can see the "real" position of the alpha-carbon is not  
> exactly on the ribbon.  Sometimes it will seem to float away, and the  
> image might not look good.  That is because the default ribbon is a  
> smooth interpolation.
>
> Possible ways to handle this issue:
>
> (a) don't show ribbon
>
> (b) make the alpha-carbon sphere(s) big enough and/or change the viewing  
> angle so it is not obviously floating away from the ribbon.  Whether  
> this is possible depends on which positions you are displaying and the  
> specific backbone conformation in those areas.
>
> (c) change the ribbon from the default B-spline to cardinal spline, with  
> or without some compromise smoothing, for example with commands:
> ribspline cardinal
> ribspline cardinal smooth strand
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>
>
> More discussion/explanation of this issue:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>
>
> 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
>
>
>


-- 
Feixia Chu, Ph.D.
Assistant Professor
Biochemistry Graduate Program Coordinator
Molecular, Cellular & Biomedical Sciences
University of New Hampshire
Gregg Hall, Rm436
35 Colovos Rd
Durham, NH 03824
Tel 603 862 2436


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