VMD-L Mailing List
From: Rune Thomas Kidmose (rtk_at_mbg.au.dk)
Date: Fri Sep 15 2017 - 05:36:46 CDT
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Hi,
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?
Cheers
Ruki
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