[Chimera-users] select

Tom Goddard goddard at sonic.net
Tue Oct 4 11:11:59 PDT 2011

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.


>         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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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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