[Chimera-users] Reducing the map to a cubic box

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 17 13:44:11 PDT 2015

Hi Sushree,
“vop boxes” will make a box of your map that includes atoms from an atomic structure or marker(s) (essentially fake atoms created with the Volume Tracer tool).  

As described in the manual page (link above), the map model is the first model number, and the second model number is the one for your open, existing atomic structure or marker(s).  I suspect you don’t have any markers or atomic structure, or if you do, maybe one or the other of your specified model numbers is not correct.  That’s my best guess, anyway!
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 15, 2015, at 12:57 PM, Sushree Tripathy <sushreet at buffalo.edu> wrote:

> Hi,
> I went through the chimera user's guide and as per the syntax used  "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map.
> Please help.
> Thanks
> Sushree.

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