From: Bylund, Tatsiana (NIH/NIAID) [F] (tatsiana.bylund_at_nih.gov)
Date: Thu Mar 03 2016 - 13:38:59 CST

thank you so much!
________________________________
From: Ryan McGreevy [ryanmcgreevy_at_ks.uiuc.edu]
Sent: Thursday, March 03, 2016 2:36 PM
To: Bylund, Tatsiana (NIH/NIAID) [F]; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: how to analyze fitting structure into density map

With such large negative values, my guess is you incorrectly calculated the ccc with the potential map (the output from mdff griddx that you used in NAMD) instead of the original density map. The potential is inverted from the density, giving you the negative numbers. If you recalculate the ccc with the density, you will likely see similar numbers, but positive, therefore indicating an improved fit.

On Thu, Mar 3, 2016 at 1:18 PM Bylund, Tatsiana (NIH/NIAID) [F] <tatsiana.bylund_at_nih.gov<mailto:tatsiana.bylund_at_nih.gov>> wrote:
if my ccc goes from -0.8 to -0.88 from start to finish (5'000 frames), does it mean that the density map wasn't fitted very well?

thank you!
________________________________
From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] on behalf of Bylund, Tatsiana (NIH/NIAID) [F]
Sent: Wednesday, March 02, 2016 7:58 PM
To: Ryan McGreevy; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>

Subject: Re: vmd-l: how to analyze fitting structure into density map
That it awesome!!!

I need to be more careful reading options.

Thank you so much, Ryan!!!!

From: Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu<mailto:ryanmcgreevy_at_ks.uiuc.edu>>
Date: Wednesday, March 2, 2016 at 7:51 PM
To: "Bylund, Tatsiana (NIH/NIAID) [F]" <tatsiana.bylund_at_nih.gov<mailto:tatsiana.bylund_at_nih.gov>>, "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>" <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: Re: vmd-l: how to analyze fitting structure into density map

f mdff check. e.g., -frames 0:10:4999 would compute the correlation for every 10th frame, starting with the first and ending at the last, but you still get a good idea of how the correlation progresses. Also, in the next VMD release (1.9.3), mdff check -ccc will be much faster in general.