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.ht...> 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@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>

Hi Hongtao, Are you talking about showing an approximately icosahedral virus, like a phage with a tail? In any case the picture you show was made with the Chimera flatten icosahedron tool and it rearranges whole protein model surfaces in this unfolded icosahedron. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/flatten/flatten.ht... <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/flatten/flatten.ht...> Each of the proteins is just repositioned without distortion. It can't be done in the same way with a cryoEM map -- that would require some projection to make the triangular facets which will involve some distortion and also will need to be done in a special way so they match at the neighboring triangle edges. One way to do that would be to chop the cryoEM map surface into 20 triangular cone pieces from the origin out through the 20 faces of an icosahedron. Then just lay out those 20 pieces as shown in the figure by rotating and repositioning them. Tom

On Mar 12, 2020, at 12:27 PM, Hongtao Zhu <zhho@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>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>