VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Mon Feb 16 2015 - 21:19:19 CST

Dear Users,

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,

Kevin
PhD Candidate
Department of Physics and Material Science
City University of Hong Kong
ukevi_at_gmx.hk