VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 05 2019 - 16:44:33 CST

Hi,
  When comparing cross correlation calculations, it is important to be sure
the same atom radii and masses are assumed by both programs, as these
values impact the calculation of the "simulated" density map that is used
for the cross correlation calculation. One can eliminate these differences
by computing a simulated density map and doing a map-map cross correlation,
and then I would expect different software to produced identical results
assuming the same input maps, thresholding etc.

Best regards,
  John Stone

On Tue, Dec 03, 2019 at 05:12:45PM +0000, Vermaas, Joshua wrote:
> Hi Paula,
>
> Are they using the same density maps in the comparisons? It could well be
> that different maps are being computed between the two programs, or that
> they use different methods for interpolating the density between points. I
> don't know enough about how Phenix is coded to provide more useful details
> than that. :(
>
> -Josh
>
>
>
> On 2019-12-03 08:36:48-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Hi!
>
> I estimated the cross correlation with both voltool/volutil and Phenix and I get the different values (0,75 and 0,85).
>
> I would like to understand what is the difference in terms of calculations and why do they differ so much, as I checked the formulations in both cases. It seems they use the same formulation.
>
> Does anyone have perhaps more information about it?
>
> Thank you
> Paula 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/