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From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Feb 17 2015 - 16:13:02 CST
If I understand correctly, your CCC is fine. The griddx map is inverted (zero becomes 1 and vice versa), which means it's now *anti*correlated to your structure. -1 is perfect anti-correlation, +1 is perfect correlation, and 0 is no correlation.
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Thanks so much for the reply.
Your guess is right, I'm in fact using the potential map generated by griddx command. However what was because I have used it for my previous (not yet trimmed) structure and CCC calculations and it seems fine as I got values of 0.7~0.8. I'm confused why the sign reverses, which indicates a rather bad correlation, simply because I trimmed the system (of cause I run new MDFFs for the trimmed ones).
I'm willing to try my very original density map instead however it has .mrc as extension and I didn't find it available in the plugin's input list.
Thanks in advance,
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The threshold is based on the map simulated from your structure. When you calculate the correlation, are you sure that you are comparing to the density map, and not the potential map (the map you fit to during mdff, created with the griddx command)? In cases of such bad correlation, my first guess is that you are using the potential instead of the density during analysis.
I am now using mdff plugin to analyse my mdff results.
I am using a quite crude density map (as it is trimmed from a much bigger one) in which there are much unoccupied density areas. As the unoccupied areas are few angstroms away from my structure, I hope they won't affect much. Therefore I resort to local ccc calculations. I have chosen threshold of 0.5 (and waiting for results of 0.2) however it still gives a very bad ccc, say -0.7 to -0.8. I am curious that the threshold was referred to the given density map or the simulated one from my input structure? If it is the given one, then the bad ccc values come from the unoccupied areas in the simulated map, right?
Thanks in advance,