From: Rune Thomas Kidmose (
Date: Fri Sep 15 2017 - 05:36:46 CDT


I have been playing around with MDFF in different versions of VMD (1.91 &1.93).

In VMD v.1.91 the MDFF plugin I use is v. 0.2

In VMD v.1.93 the MDFF plugin I use is v. 0.5

When running the following CCC calculations on the same input pdb and map I get different results in one of the cases:

mdff ccc (atomselection of whole protein) -i map.mrc -res 2

VMD 1.91: = 0.649038

VMD 1.93: = 0.649038

mdff check -ccc (whole protein) -map map.mrc -res 2 -cccfile output.txt

VMD 1.91: = 0.646135

VMD 1.93: = 0.5732

I state no thresholds in either case so I believe I am calculating global CCC values.

So I was wondering why I see this discrepancy in CCC values between the different VMD (and MDFF) versions, when using mdff check -ccc, and which I should assume to be "correct"?

Is the easy answer to just use mdff ccc instead of mdff check -ccc?