[Chimera-users] Fit in map equivalent for surfaces?

Elaine Meng meng at cgl.ucsf.edu
Sat Nov 26 11:43:49 PST 2016

Hi Joe,
The fitting uses the actual map values, although you can delimit them by a surface.  So, I’d say there isn’t really a way to use the envelope or surface only, without the interior values.  However, you could use “molmap" to simulate density maps from the two atomic structures and then use the map-map fitting.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 26, 2016, at 7:49 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:

> Hi Chimera Team,
> Is it possible/does a function exist to fit one structure inside the calculated surface of another?
> To be clear, i don't mean inside a density map, I mean an MSMS surface calculated from a PDB inside chimera itself.
> I have 2 proteins that are sequentially very different, but I suspect fulfilling the same role. They don't overlay via MatchMaker well, but they look to have quite similar space occupation, so I'd like to see how well they fit in one anothers 'map'.
> Any alternative suggestions appreciated!
> Thanks,
> Joe

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