VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Tue Mar 01 2016 - 11:09:45 CST

As discussed in the tutorial, you can calculate a global cross correlation
between your structure and your density map using 'mdff check' or mdff
'ccc'. This value will give you an idea of the quality of fit. You can also
use Timeline to calculate many local cross correlations which will provide
a finer level of analysis. Using Timeline for cross correlation is
discussed in the last section of the mdff tutorial.

On Tue, Mar 1, 2016 at 10:45 AM Bylund, Tatsiana (NIH/NIAID) [F] <
tatsiana.bylund_at_nih.gov> wrote:

> Dear all,
>
> I performed fitting of a protein structure into a density map. I followed
> mdff tutorial, but in my case I don't have the target structure, just the
> initial structure and target density map.
>
> Is there a way to analyze the results? Not sure how to compute rmsd since
> there is no target structure.
>
> Thank you very much!
>
> Best regards,
> Tatsiana
>
>