Crystallographic Map Expansion
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 www.nanoimagingservices.com
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@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
Hi Elaine, That works perfectly. Thank you for your help! Best, Jessica On Fri, Jul 24, 2020 at 11:44 AM Elaine Meng <meng@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@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 www.nanoimagingservices.com
participants (2)
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Elaine Meng -
Jessica Bruhn