Creating a cubic box for a density map
Dear Chimera users When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM? Thanks Juan -- Juan Luis Loredo Varela PhD Student Antson Group York Structural Biology Laboratory L0 Department of Chemistry University of York
Dear Juan, Take a look at the command “vop cover” with box, ibox, or fbox option. I think that will do what you want: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> 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 Jan 18, 2015, at 7:55 AM, Juan Luis Loredo Varela <jlvl500@york.ac.uk> wrote:
Dear Chimera users When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM? Thanks Juan
Hi Juan, The Chimera Segger dialog menu entry Regions / Extract Densities let’s you make cube shaped maps for selected segmented regions. I guess you were using Segger menu File / Save Selected Regions which does not give that option. Tom
On Jan 18, 2015, at 7:55 AM, Juan Luis Loredo Varela <jlvl500@york.ac.uk> wrote:
Dear Chimera users
When I use the Segment map option to save a specific fragment as .mrc file, Chimera uses the minimal box containing the segment. Does anyone know how to modify the dimensions of a density map to have it in a cubic box that can be used in Flex-EM?
Thanks
Juan
-- Juan Luis Loredo Varela
PhD Student Antson Group York Structural Biology Laboratory L0 Department of Chemistry University of York _______________________________________________ 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 -
Juan Luis Loredo Varela -
Tom Goddard