[Chimera-users] Multiple fitting of structures in to EM densities

Healey, Joe J.R.J.Healey at warwick.ac.uk
Tue May 9 08:07:48 PDT 2017

Dear chimera team,

I have a large EM density I would like to fully populate with a number of copies of a protein. To be more specific, the EM density is of 2 concentric protein rings (EMDB-6720), and each concentric ring is stacked 3 or 4 times. Each ring is a hexamer, so I would like to populate every single ring with 6 copies of each protein (but the inner and outer rings are 2 different proteins).

What would be the best mechanism to iteratively import a protein, populate an EM density space, then move on to the next one? Currently, I think if I was to simply open several copies of the protein, they would probably all try to fit within the same EM density position, leaving the rest of the structure empty?

My apologies if this isn't totally clear, I've tried to explain it as best as I think I can. I'm happy to accept solutions in 'chimera language', python (or I also have Jaime's Pychimera installed).

Many thanks

Joe Healey

M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170509/5db548e6/attachment.html>

More information about the Chimera-users mailing list