[Chimera-users] Depiction of backbone CA atoms as spheres

George Tzotzos gtzotzos at me.com
Sat Nov 5 12:33:20 PDT 2016


Thank you Elaine,

Extremely helpful as always. Have a good weekend

George

> On 5 Nov 2016, at 19:21, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi George,
> You didn’t say what you meant by “didn’t work” but I’m guessing the CA atoms did not display.  This is because by default, showing ribbon suppresses display of the backbone atoms (N,CA,C,O).  First allow showing both ribbon and backbone atoms with command:
> 
> ribbackbone
> 
> …and you might still need to display the specific CA atoms you want, for example:
> 
> disp sel & @ca
> disp :77-80 at ca
> …if the residues were selected (first example) or to specify residue numbers directly (second example)
> 
> …and if the CAs are connected with each other by straight lines, turn that off with
> 
> setattr m autochain false
> 
> ...and then use the commands you showed earlier:
> 
>> repr bs @ca
>> vdwdefine +1.0 @ca
> 
> The vdwdefine makes the balls larger so that it’s less obvious where the CA atoms are offset from the ribbon.  You wouldn’t have to use exactly that value, but in general it is a good compromise.
> 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 Nov 5, 2016, at 8:56 AM, George Tzotzos <gtzotzos at me.com> wrote:
> 
>> I’m trying to depict selected backbone atoms as spheres with a smaller vdw radius. Residue side chains should not been shown. I checked the list and found an option that appears to do the job, e.g
>> 
>> sel :77-80, 91-94
>> repr bs @ca
>> vdwdefine +1.0 @ca
>> 
>> But this didn’t work for me.
>> 
>> Grateful for any suggestions
>> 
>> Thanks in advance
>> 
>> George
> 




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