VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed May 24 2017 - 09:16:19 CDT

(1) In general those values are pretty low. Having a high of .35 is not
very good. The extremely low negative values are most likely due to pieces
of the structure that are sticking out of the map significantly, where
correlation is undefined. You could also try using the "threshold" option
in the Timeline cross correlation parameters (try 0.1 for example) which
will remove some of the excess noise around your structure from the
calculation. Is your structure that you are analyzing the result of a
fitting, like MDFF? Without actually seeing the map and model it is hard to
say anything more concrete.

(2) It is okay that Timeline and mdff ccc do not give exactly the same
results. First, if you ran Timeline with default options, the correlations
are calculated on sections of contiguous secondary structure, not
per-residue, so the CC's are not being calculated on exactly the same
parts. Second, the algorithms used by the Timeline and mdff ccc are not
exactly the same, so there will be small discrepancies, but shouldn't be
more than a few hundredth.

On Wed, May 24, 2017 at 2:50 AM Karol KASZUBA <karol.kaszuba_at_ist.ac.at>
wrote:

> Hi,
>
> I am trying to calculate the cross-correlation score between my map and a
> model. The map is in .mrc format.
>
> (1) At first I used time line plugin and "calculate cc" option.
> So, I got the scores. They make sense, but what I am worried is the scale:
> it starts from -100 and finishes at 0.35. Is it normal?
>
> I would expect a score from 0 to 1, where low values would correspond to
> poor density fit, while higher (positive) values would denote a good match.
>
> (2) I also calculated cc using "mdff ccc" command in tcl console. I just
> choose one residue to see whether the cc score calculated in time line
> and from command line. will be the same. These were not.
>
>
> Please let me know what do you think
> thanks
> Karol
>
>