Hi Pradeep,
That message is saying you must specify the density map. I.e. if the atomic structure is model #0 and the density map is model #1, the command could be something like
vop cover #1 atom #0
Command usage and options:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>
Elaine
-----
Elaine C. Meng, Ph.D.P.S. it is recommended you send Chimera questions to chimera-users@cgl.ucsf.edu instead of to me directly - thanks!
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Sep 18, 2013, at 2:02 PM, Pradeep Pallan wrote:
> Hi Elaine,
>
> I was looking at using vop cover. I have a case where part of the molecule
> is not within electron density box. The map cuts off at the unit cell dimensions,
> and my space group is P1. Where I need edensity is approximately at y= -10.
> When I try the command
> 'vop cover "atom"', it gives the message "file.pdb is not a volume".
>
> Is this the right way of getting the molecule covered in e density or do I need
> to use a different option.
>
> Thank you,
> PP