VMD-L Mailing List

From: Bylund, Tatsiana (NIH/NIAID) [F] (tatsiana.bylund_at_nih.gov)
Date: Wed Mar 02 2016 - 18:05:34 CST

Oh, it actually works now. I have 5'000 frames and it's slow.

Thank you so much!!!!

From: Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu<mailto:ryanmcgreevy_at_ks.uiuc.edu>>
Date: Wednesday, March 2, 2016 at 12:28 AM
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

What version of VMD and what operating system are you using? Also, do you get any messages or errors in the VMD terminal (the one you started VMD in) when you run the command?

On Tue, Mar 1, 2016 at 6:54 PM Bylund, Tatsiana (NIH/NIAID) [F] <tatsiana.bylund_at_nih.gov<mailto:tatsiana.bylund_at_nih.gov>> wrote:
When I tried

Mdff check –ccc ….

It said calculating the cross correlation, but then no window appeared and console got to the next command without making any output.

Do you know where can be the problem?

Thank you very much!

Best regards,
Tatsiana

From: Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu<mailto:ryanmcgreevy_at_ks.uiuc.edu>>
Date: Tuesday, March 1, 2016 at 12:09 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

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<mailto: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