Hi María, To mask the virus particle to a spherical shell you would create the spherical shell with the "shape sphere" command and do the masking with the "mask" command. This will create ugly stair-step artifacts where the density crosses the spherical surface and I don't have a good way to eliminate those. Here are the commands for EMDB 1123 open emd_1123.map volume #0 originIndex 297 level 400 shape sphere radius 315 coord #0 slab 0,20 color pink mask #0 #1 volume #2 step 1 and I've attached two pictures. The second command sets the center of the origin of the map to the center of the virus and sets the contour level. The shape command makes a spherical shell centered on the map origin of radius 315 to 335. The mask command creates a copy of the map setting density outside the spherical shell to 0. The last command shows the resulting map at full resolution. Details of all the commands are in the Chimera User's Guide. This comes with Chimera. For example, you can use Chimera command help shape to show documentation in a web browser for the shape command. Tom
Hello,
I working about Bam35c virus (emd_1123.map). That virus has a capsid and other things inside. I want used only exterior part (between 315 and 335 amstrons) and discard other parts. How can I select only this external part?
Thank you for your help
María
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