Thanks, Elaine. It worked, I will make sure I will send an email to the users list next time. Thanks! PP On Wed, Sep 18, 2013 at 4:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

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. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

P.S. it is recommended you send Chimera questions to chimera-users@cgl.ucsf.edu instead of to me directly - thanks!

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

-- ------------------------------------------------------------------- Pradeep Pallan