VMD-L Mailing List

From: Bylund, Tatsiana (NIH/NIAID) [F] (tatsiana.bylund_at_nih.gov)
Date: Thu Mar 03 2016 - 13:17:52 CST

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 [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
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.