Hi Megan, The "vop cover" command (actually "volume cover" in ChimeraX, but both will work) needs both the map model number and the atomic model number. So if your map model is #1 and the atomic model is #2, maybe something like:
volume cover #1 atomBox #2
You can see the help for "volume cover" by using the command "help volume cover" ... or the same thing on our website here: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover
That manual page shows the command syntax and explains the options. The "volume-spec" in the usage is the map model number.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 28, 2020, at 7:42 AM, Megan Mayer mmayer@nanoimagingservices.com wrote:
Hi chimeraX forum,
I am trying to get an electron density map (.mrc) to overlap with atomic structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule.
I am thinking to use the "vop cover" command to get the density to expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response.
Thanks in advance for any help!!
Megan