[Chimera-users] Crystallographic Map Expansion

Jessica Bruhn jbruhn at nanoimagingservices.com
Fri Jul 24 12:17:33 PDT 2020

Hi Elaine,

That works perfectly. Thank you for your help!


On Fri, Jul 24, 2020 at 11:44 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Jessica,
> As I understand it, Coot may automatically use symmetry to display the map
> so that it covers the atomic structure.
> In Chimera, the map isn't automatically extended or translated to cover
> the atoms, but you can do so using the "vop cover" command:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jul 24, 2020, at 9:12 AM, Jessica Bruhn <
> jbruhn at nanoimagingservices.com> wrote:
> >
> > Hi,
> > I am trying to open a map generated by microED. I generated a SigmaA map
> in coot based on an fcf file generated by SHELXL (see attached). I can open
> it in Chimera and things look reasonable. I am wondering if it is possible
> to expand the density map beyond the boundaries of the available box using
> the crystallographic symmetry? Additionally, I am a bit confused by the
> size of the box. I would have expected it to have the dimensions of the
> unit cell or the asymmetric unit, but it does not appear to be either of
> those. The map does appear to be scaled properly.
> >
> > Any help would be greatly appreciated.
> > Thanks,
> > Jessica

Jessica Bruhn, Ph.D
Principal Scientist
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
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