[Chimera-users] vop cover

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 18 14:09:50 PDT 2013


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 at 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




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