[Chimera-users] Using vop to cover a whole molecule

Pradeep Pallan pradeeppallan at gmail.com
Mon May 22 10:27:13 PDT 2017


Thank you, Tom.
Pradeep

On Mon, May 22, 2017 at 12:24 PM, Tom Goddard <goddard at sonic.net> wrote:

> The problem was the map file had symmetry operators using lowercase x,y,z
> in the symmetry operators in the CCP4 file header and Chimera only parses
> uppercase X,Y,Z.  When I open your map I see in the Chimera reply log the
> following warning
>
> Unable to parse symmetry operators of dnaxraydata.map
> x, y, z
>      x+1/2, -y+1/2, -z
>          -x, y+1/2, -z+1/2
>              -x+1/2, -y, z+1/2
>
> Since it can’t read the 4 symmetry operators the vop cover command only
> uses unit cell translational symmetry.    I see using “volume #0 dumpHeader
> true” a comment in the map header saying “From clipper Xmap”.  So I guess
> that software writes lowercase x, y, z.  I’ve changed Chimera to accept
> upper or lower case symmetry operators.  This will be in tonight’s Chimera
> daily build.  Thanks for reporting the problem.
>
>         Tom
>
> > On May 19, 2017, at 4:48 PM, Tom Goddard  wrote:
> >
> > Hi Pradeep,
> >
> >  Maybe your xray density map is not a full asymmetric unit so the whole
> unit cell cannot be reconstructed from it.  Or maybe the symmetry operators
> aren’t in the map file so it is only using unit cell translations.  Can’t
> be sure what the problem is without access to the specific data files.
> >
> >       Tom
> >
> >> On May 19, 2017, at 11:37 AM, Pradeep Pallan wrote:
> >>
> >> Hi All,
> >>
> >> I would like to know how to extend an e-density map
> >> in y or z direction. Here is my case:
> >>
> >> The DNA structure that was refined in shelx.
> >> Model #0 is DNA and the e-density map is model #1.
> >> When I used vop cover #1 atom #0, the electron density
> >> covers the molecule along two axes, and for the third axis
> >> it covers partly. How to extend the e-density map in a particular
> >> axis?
> >>
> >> Thank you!
> >> --
> >>
> >> -------------------------------------------------------------------
> >> Pradeep Pallan
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> >
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>


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