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channotation / chap

CHAP is a tool for the functional annotation of ion channel structures:
http://www.channotation.org
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Plot against z-coordinates #44

Open askusay opened 2 years ago

askusay commented 2 years ago

Hi CHAP team,

I have 2 CHAP profiles for two aligned ion channels.

The channels are different in height and therefore have different centres of mass but their channels are aligned. when I plot their profiles they are not aligned, presumably because of the difference in them COMs.

I typically plot the radius against data["pathwayProfile"]["s"]. Would it be possible to plot against the z-coordinate? All simulation frames are aligned

Thanks

DSeiferth commented 2 years ago

Unfortunately, there is no option to change the pathway coordinate from COM to z-coordinate. In future releases of CHAP, we plan to add this feature.

Regarding your plots: You could find the z-coordinate of the COM of the structures (for example with MDAnalysis) and shift the data["pathwayProfile"]["s"] array by adding constants such that the radius profiles are aligned.