[chimerax-users] help please - electrostatic potential units and fit in map correlation

[Leslie Bridges]

that's extremely helpful, many thanks

Dr Leslie R Bridges
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 12 December 2022 23:16
To: Leslie Bridges <lbridges at sgul.ac.uk>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] help please - electrostatic potential units and fit in map correlation

Dear Dr Leslie Bridges,

(1) if you mean the electrostatic potential from the "coulombic" command (or the icon that runs it), the units are kcal/(mol·e) at 298 K.

"coulombic" help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html>

If you mean that you calculated a map in some other program like DelPhi or APBS then opened it in ChimeraX, then the units are whatever that other program outputs, so you would need to check its documentation.

(2) as I understand it, there are many variables like the amount of noise in the map and its resolution that can affect the correlation value, so it is really just for comparing different fits of the same structure in the same map.  Thus there is no agreed-upon universal value that signifies a good fit, it is merely that given a particular set of atoms and particular map, higher correlations would represent better fits than lower correlations.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 12, 2022, at 3:06 AM, Leslie Bridges via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear All
>
> What are the units for electrostatic potential in ChimeraX?
>
> Is it possible to say whether the fit in map correlation represents a "good" fit for the atoms (e.g. if my correlations are above 0.75, can I conclude all the fits are good?)
>
> All the best, thanks
>
> Dr Leslie R Bridges
> Hon Snr Lecturer in Neuropathology
> St George's University of London

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