VMD-L Mailing List

From: Karol KASZUBA (karol.kaszuba_at_ist.ac.at)
Date: Wed May 24 2017 - 02:49:25 CDT

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