Hi Abhi, The ChimeraX command "measure correlation" will report the correlation coefficients between two maps. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#correlatio... If you are trying to compare atomic models then you need to convert those into a density map to compute correlation and the ChimeraX molmap command does that. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html Tom

On Jul 14, 2023, at 8:21 AM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi ChimeraX community:

I’m trying to get real space correlation coefficient value of map-model fit as done in this paper from DiMaio’s grouphttps://elifesciences.org/articles/17219 (Table 2, RSCC validation map column). It is possible to do so in Chimera but I’m not sure how. Although the alternative might be the Map-Q & Q-score plugin in chimera (or Model-Map Q score in ChimeraX) from Greg Pintilie which “uses a real-space correlation approach to assess the resolvability of each model atom in the map” (-http://doi.org/10.1038/s41592-020-01051-w), I would like to get the RSCC values. Is it possible to obtain those values? Thanks in advance for any advice.

-abhi

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