VMD-L Mailing List

From: Lizelle Lubbe (LBBLIZ002_at_myuct.ac.za)
Date: Thu Nov 23 2017 - 06:21:07 CST

Hi Alvaro,

Thanks for the rapid reply and sending this script.

I meant that the colourplot you get when using the Timeline tool in VMD does not show up. It is meant to enable interactive visualization of the structural changes accompanying SASA fluctuation.

After some tinkering it seems like the calculation is successful when selecting sequential residues (eg. resid 1 to 300) but fails when using selection: same residue as within 13 of resname ZN1.
This selection is preferred due to the memory-intensive nature of SASA calculation over a large number of frames.

Your script might cope better with this selection
Can the results be plotted as a colourscaled map over time? (i.e. x-axis = time, y-axis = residue with each residue as a coloured block)

Kind regards

Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town

________________________________________
From: Alvaro Lopez <alvarojh123_at_gmail.com>
Sent: 23 November 2017 01:23:17 PM
To: Lizelle Lubbe
Subject: Re: vmd-l: Timeline SASA

Hi. I dont understand wheny you said about heatmap generation.

But if you want to calculate the temporal evolution of SASA it is very easy. I attach a tcl script that I used(I hope that you have experience with tcl).
In SELECTION put the residues that you want to consider in SASA calculation.

set sel [atomselect top "SELECTION"]
set protein [atomselect top "protein"]
set n [molinfo top get numframes]
set output [open "SASA.dat" w]
# sasa calculation loop
for {set i 0} {$i < $n} {incr i} {
        molinfo top set frame $i
        set sasa [measure sasa 1.4 $protein -restrict $sel]
        puts "\t \t progress: $i/$n"
        puts $output "$sasa"
}
puts "\t \t progress: $n\$n"
puts "Done."
puts "output file: SASA.dat"
close $output

2017-11-23 8:48 GMT-02:00 Lizelle Lubbe <LBBLIZ002_at_myuct.ac.za<mailto:LBBLIZ002_at_myuct.ac.za>>:
Hi all,

I would really like to calculate the fluctuation in residue SASA over time using the Timeline tool.
When loading a prmtop and nc file the calculation proceeds to 100% but in the terminal shows :

Timeline is checking sequence info for molecule
Timeline couldn't find a sequence in this molecule

The simulated protein is a glycosylated zinc metalloprotease. I used custom metal site parameters and therefore altered these residues' names (HIR, HIT = HIS and GLR = GLU)
Could the custom names or glycans be preventing the heatmap generation?

Any idea as to how I could successfully obtain a residue SASA vs time plot?

Kind regards

Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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