VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Feb 01 2017 - 01:44:51 CST

No. The restrict flag is used to measure the sasa of only a selection, by still considering blocked surface area by other parts of the molecule. So when selecting “protein” to measure sasa and use “-restrict” on a special resid, you obtain only the surface of that special resid that is not blocked by the rest of the protein. This is different from measuring the surface of only that resid.

 

Norman Geist

 

Von: Anna Battisti [mailto:battistianna_at_googlemail.com]
Gesendet: Dienstag, 31. Januar 2017 18:30
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: vmd-l: SASA area

 

I do not think the problem is on "-restrict“ flag
because in true exists also considering just a single atom, eg a C atom in the file:

file.pdb:
ATOM 5 CA THR 1 32.140 62.910 61.880 1.00 0.00

 

In this case the area calculated with vmd is correct:

vmd > set atom [atomselect top "index 0"]
atomselect0
vmd > measure sasa 1.4 $atom
105.68318176269531

while considering the precessed file (file.1000)
   1 1.5000 32.1400 62.9100 61.8800

 

./surf_LINUXAMD64 -W 1 -R 1.4 file.1000

the sum of the area of the triangles is

26.6884683024564

 

 

On Tue, Jan 31, 2017 at 4:35 PM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

This looks ok so far, but inside VMD you use the „-restrict“ flag to obtain the surface residue based. How do you do the same when using the external tool? So it’s reasonable you get different results.

 

Von: Anna Battisti [mailto:battistianna_at_googlemail.com <mailto:battistianna_at_googlemail.com> ]
Gesendet: Dienstag, 31. Januar 2017 12:31
An: Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> >
Betreff: Re: vmd-l: SASA area

 

Thanks a lot for replying!
Sorry, what do you mean? maybe the flag I used?
 ./surf_LINUXAMD64 -W 1 -R 1.4 fort.1000

Anyway, step by steps, I have done the calculation in the following way:

1) starting from pdb file I generated the fort.1000 file:

awk 'BEGIN{while((getline < "output_VMDradius.dat")>0){n++; a[n]=$1}}{printf "%4i%10.4f%10.4f%10.4f%10.4f\n",NR,a[NR],$6,$7,$8}' temp2 > fort.1000

the beginning of the file is:

   1 1.4000 31.3700 63.3600 63.0500
   2 1.5000 32.1400 62.9100 61.8800
   3 1.5000 31.2900 61.9600 61.0200
   4 1.5000 32.1000 61.0600 60.1400
   5 1.3000 30.4700 61.2400 61.9500
   6 1.5000 32.6000 64.1100 61.0600
   7 1.3000 31.9900 65.1700 61.1500
   8 1.4000 33.6700 63.9300 60.2900
   9 1.5000 34.2400 65.0600 59.5500
  10 1.5000 35.6200 65.3500 60.1900
  11 1.5000 36.6100 65.9800 59.2900
  12 1.3000 35.4200 66.2000 61.3300
--------

The first column is the number of the line, the second is the VDW radius (calculated with VMD) then the coordinates (x, y, z)

2) Then I processed the fort.1000, and obtained fort.1000.tri in this way:

./surf_LINUXAMD64 -W 1 -R 1.4 fort.1000

 

 

3) I calculated the area of the triangles of the triangles.

Is this procedure correct?

 

 

On Tue, Jan 31, 2017 at 12:05 PM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

How did you tell the surf_LINUXAMD64 the restrict settings that you used in the TCL version?

 

Von: owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu> [mailto:owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu> ] Im Auftrag von Anna Battisti
Gesendet: Dienstag, 31. Januar 2017 08:28
An: vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
Betreff: vmd-l: SASA area

 

Dear all,

 

I'm doing the sasa area calculation but something strange is happening: I'm seeing different results by comparing the calculation made with

 

set output [open "output_SASA.dat" w]

for {set x 0} {$x <= 2084} {incr x} {

set sel [atomselect top "index $x"]

set protein [atomselect top "protein"]

  set sasa [measure sasa 1.4 $protein -restrict $sel]

  puts $output "$sasa"

}

close $output

 

and that I obtained calculating the area of each atom as sum of the associated triangles area, when the triangles are obtained with:

 

./surf_LINUXAMD64 -W 1 -R 1.4 file > file.tri

 

I have supposed that the procedure to calculate the sasa with VMD is the same , namely surf_LINUXAMD64 is the VMD program.

 

Kindly, could you give me any kind of suggestion or tell me if there is some specific approximation?

 

Thanks

 

Anna