[Chimera-users] coloring by RMSD (conformational variability)

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 6 14:43:38 PDT 2016


Hi George,
Oh, I see… each model is just a tube, but together they form fanlike structures, similar to output from the ViewMotions server:
<http://viewmotions.bc.edu/>

Thanks for sharing!
Elaine

> On Jun 6, 2016, at 1:13 PM, George Tzotzos <gtzotzos at me.com> wrote:
> 
> Hi Elaine,
> 
> Grateful for the prompt and useful response.
> 
> The flat ribbons come for a cluster of pdb files sampled from the first eigenvector of PCA. I’m attaching such a file.
> 
> Once again, many thanks
> 
> George
> <pc1.pdb>
> 
>> On 6 Jun 2016, at 21:55, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi George,
>> I’m not really sure how you got those flat ribbons, but I think you can just use the transparency command.  It takes a percentage transparency, so for 75% transparent, a command something like:
>> 
>> transp 75,r  :1-10,124-125
>> 
>> … where the “,r” part does NOT have any space before it, and “r” stands for ribbons.
>> 
>> I hope this helps,
>> Elaine




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