[Chimera-users] Fit list behavior query

Oliver Clarke olibclarke at gmail.com
Sun Oct 27 12:32:37 PDT 2019


I often use fitmap with the “search” flag to find the orientation of a fragment (e.g. a single domain of a larger protein) in a cryoEM map - something like “fitmap #1 #0 search 100 radius 5”. Normally, a fit list table will appear and the model will reorient to match the highest scoring entry in the fit list.

One thing I have noticed is that if I run a second such command after the first (e.g. to try a different radius or number of trials), the fit list is not updated - all the entries are identical, and the model is again reoriented to match the highest entry in the first list. I find I need to first manually clear all the fits from the first trial in order for it to correctly update with the results of the second run.

I wonder if it would be possible to alter this behavior such that the fits from the first run are automatically cleared if a second fitmap command is issued?


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