[chimerax-users] flatten a cryoEM map

[Hongtao Zhu]

Hi Elaine and Tom,

Thanks for your answers. I appreciate this. It seems that I need to do this by other software or do it manually. 

Thanks,

Hongtao

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Thursday, March 12, 2020 2:29 PM
To: Hongtao Zhu <zhho at ohsu.edu>
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] flatten a cryoEM map

Hi Hongtao,
ChimeraX doesn't have a tool to do this, but you can use the "Flatten Icosahedron" tool in Chimera to make this kind of image for icosahedral viral capsids:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/flatten/flatten.html>

It works on the low-resolution chain surfaces generated by the Chimera tool "Multiscale Models" from the atomic structure of the asymmetric unit -- not the EM map surface, as far as I know, and only for a specific orientation of icosahedral symmetry.

I have seen flattened images of map surfaces in papers, but suspect that they were made with some other program (not Chimera or ChimeraX).
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 12, 2020, at 12:27 PM, Hongtao Zhu <zhho at ohsu.edu> wrote:
> 
> Hi there,
> Could you show me how to flatten a cryoEM map in chimera just like the attachment? My map has several subunits but with C1 symmetry. 
> Thanks, 
> Hongtao
> <Image.png>