help please - electrostatic potential units and fit in map correlation
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
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@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
that's extremely helpful, many thanks Dr Leslie R Bridges ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 12 December 2022 23:16 To: Leslie Bridges <lbridges@sgul.ac.uk> Cc: ChimeraX Users Help <chimerax-users@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@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
participants (2)
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Elaine Meng -
Leslie Bridges