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
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Maria, You can't really select part of a map, but you can delete or "erase" parts of it. With the Volume Eraser tool (under Tools... Volume Data in menu), you can place a sphere on the map and erase everything outside (or inside) that sphere. However, that requires moving the sphere by hand, which might be hard. <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html> Another possibility is to create a surface in the shape of a sphere, or icosahedron, or sphere-icosahedron blend with specified center using the "shape" command, and then use the "mask" command to erase outside that surface. I'm not sure if the masking gets the inside or outside by default, but there is a keyword to invert so you will be able to both. <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> Actually I don't know what shape that virus is. The above assumes something roundish or icosahedral. The "shape" command includes other shapes, but if the virus is irregular, it may be necessary to use some other program to create a surface of the shape needed for masking. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 3, 2011, at 8:16 AM, maznar wrote:
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
Hi Elaine, Thank you very much, you helped me a lot. María On Tue, 4 Oct 2011 11:13:16 -0700, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Maria, You can't really select part of a map, but you can delete or "erase" parts of it.
With the Volume Eraser tool (under Tools... Volume Data in menu), you can place a sphere on the map and erase everything outside (or inside) that sphere. However, that requires moving the sphere by hand, which might be hard. <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>
Another possibility is to create a surface in the shape of a sphere, or icosahedron, or sphere-icosahedron blend with specified center using the "shape" command, and then use the "mask" command to erase outside that surface. I'm not sure if the masking gets the inside or outside by default, but there is a keyword to invert so you will be able to both. <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
Actually I don't know what shape that virus is. The above assumes something roundish or icosahedral. The "shape" command includes other shapes, but if the virus is irregular, it may be necessary to use some other program to create a surface of the shape needed for masking.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 3, 2011, at 8:16 AM, maznar wrote:
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
maznar -
Tom Goddard