VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Fri Sep 15 2017 - 08:56:03 CDT

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 <rtk_at_mbg.au.dk> wrote:

> 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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