[Chimera-users] Visualizing SARS-CoV-2 spike protein

[Elaine Meng]

Dear Chun-Nan Chen,
As Tom Goddard suggested, it is recommended to use ChimeraX instead if you have surface calculation errors in Chimera.

However, if this is for commercial use, both programs require licensing:

<http://www.rbvi.ucsf.edu/chimerax/docs/licensing.html>
<http://www.rbvi.ucsf.edu/chimera/docs/licensing.html>

It may be different on your computer, but when I use Chimera to show surface on 6VSB, the outer surface of chain B is displayed even though there is an error message.  At least on my laptop, the failure is on some interior bubble that is not needed to display the outer surface; in the attached image, chain A is dodger blue, B is yellow, C is red.  If you don't have any surface on chain B on your computer after the error, however, the best advice is to use ChimeraX instead.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 18, 2020, at 11:53 PM, Chun-Nan Chen <chunnan.chen at singlecelltechnology.com> wrote:
> 
> Hello,
>  
> I apologize.  The PDB no. should be 6VSB.  Thank you for your assistance.
>  
> Chun-Nan Chen, Ph.D.
> CEO
> Single Cell Technology, Inc.
> 6280 San Ignacio Ave. Suite E
> San Jose, CA  95119
> Mobile: (408) 642-9741
> Email: chunnan.chen at singlecelltechnology.com
> Web: singlecelltechnology.com
>  
>  
>  
> From: Chun-Nan Chen <chunnan.chen at singlecelltechnology.com> 
> Sent: Saturday, April 18, 2020 10:45 PM
> To: 'chimera-users at cgl.ucsf.edu' <chimera-users at cgl.ucsf.edu>
> Subject: Visualizing SARS-CoV-2 spike protein
>  
> Hello,
>  
> I am trying to visualize the SARS-CoV-2 spike protein, which is a trimer (PDB no. 6CRZ).  I wish to surface chain B, which is in an “up” conformation) but it kept giving me an error message.  I tried the “split” command and other solutions without success.  I could surface just the B chain but I really want to surface all 3 chains and color the RBD.
>  
> Could anyone help me with this issue?
>  
> Thank you,
>  
> Chun-Nan Chen, Ph.D.
> CEO
> Single Cell Technology, Inc.
> 6280 San Ignacio Ave. Suite E
> San Jose, CA  95119
> Mobile: (408) 769-2171
> Email: chunnan.chen at singlecelltechnology.com
> Web: singlecelltechnology.com
>  
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