[Chimera-users] vop cover

Pradeep Pallan pradeeppallan at gmail.com
Wed Sep 18 15:15:44 PDT 2013


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 at 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 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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Pradeep Pallan
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