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

Healey, Joe J.R.J.Healey at warwick.ac.uk
Mon Nov 28 04:50:07 PST 2016

Thanks Elaine, that has done the job.

Out of curiosity, I noticed from your documentation that the fitting actually only 'kicks in' after the densities are overlaid by hand roughly first. Is there any mechanism for the objects to move to one another as in the MatchMaker function (considering automating this process)?

Alternatively, I could envisage perhaps centroiding both densities, and moving the centroids to occupy the same space, as which point fitting would take over. Any thoughts?

Joe Healey

M.Sc. B.Sc. (Hons)
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>
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 26 November 2016 19:43:49
To: Healey, Joe
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Fit in map equivalent for surfaces?

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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