From: Rune Thomas Kidmose (
Date: Wed Jan 17 2018 - 14:36:12 CST

Hi again,

After yet again playing with MDFF check for calculating CCC values, I was just wondering what the default sigma threshold value is, if none is given in the command?


mdff check -ccc -map emd_6826.mrc -res 5.8 -cccfile ccc_f001.txt


mdff check -ccc -map emd_6826.mrc -res 5.8 -cccfile ccc_f001.txt -threshold 0.5

I have not been able to find the answer online, so apologies if it is clearly stated some where and I missed it.

Any standards on which sigma value one should use when calculating the CCC via mdff check?


Fra: Ryan McGreevy <>
Sendt: 15. september 2017 15:56
Til: Rune Thomas Kidmose;
Emne: Re: vmd-l: MDFF Check -ccc in different VMD versions

mdff check -ccc in 1.9.3 uses a newer, faster algorithm for calculating the cross correlation. The discrepancy you see is because the new algorithm calculates the simulated density map differently than the old algorithm. The new algorithm is also more accurate than the old one, so the value you get in 1.9.3 is more "correct". The higher the resolution of your map, the greater the discrepancy will be. However, if for some reason you really want to use the old algorithm in 1.9.3, you can use the -deprecate flag in the mdff check command.

On Fri, Sep 15, 2017 at 6:37 AM Rune Thomas Kidmose <<>> wrote:


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?