From: Mi Yang (drmiyang2019_at_gmail.com)
Date: Wed Dec 30 2020 - 08:04:13 CST
Dear Varun,
Thanks for your comments. I am pasting the original script which I modified
and run because there was no uploading of pdb and psf files in it:
CC: Dr.Peter please see if you can comment on it to explain it to us what
is what here:
#calculation of RMSF of CA atom using superposition
#works when pdb and dcd files are preloaded using GUI(no psf #needed)
set num_frames [molinfo top get numframes]
set kk [expr $num_frames - 1]
set a [atomselect top "protein and name CA and segname AP1 and resid 14 to
377"]
set c [atomselect top "protein and name CA and segname AP1 and resid 14 to
377" frame $kk]
for {set i 0} {$i<$num_frames} {incr i} {
$a frame $i
$a move [measure fit $a $c]
}
set outfile [open "rmsf_CAxx.dat" "w"]
puts $outfile "Residue \t RMSF"
for {set i 0} {$i < [$a num] } {incr i} {
set rmsf [measure rmsf $a first 1 last $kk step 10]
puts $outfile "[expr {$i+1}] \t [lindex $rmsf $i]"
}
close $outfile
On Wed, Dec 30, 2020 at 10:45 AM varun dewaker <varun_dewaker1986_at_yahoo.com>
wrote:
> Dear Dr Mi,
> I think this script I have provided you and you have modified it according
> to your need. Here you have deleted the segname and protein residue no
> range.
> May be this will give you error.
> You can also copy paste the script here and let the Dr Peter
> comments/suggestions.
> Thanks
>
> Sent from Yahoo Mail on Android
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>
> On Wed, Dec 30, 2020 at 12:59 PM, Mi Yang
> <drmiyang2019_at_gmail.com> wrote:
> Dear Peter,
> Thanks for your encouraging reply. Please see my tcl script file which I
> used to calculate RMSF:
> I think comments part is more informative here because in my case psf was
> also there:
>
> #calculation of RMSF of CA atom using superposition
> #works when pdb and dcd files are preloaded using GUI(no psf #needed)
> mol new solvate.psf type psf
> mol addfile solvate.pdb type pdb
> mol addfile output.dcd type dcd first 0 last -1 step 5 waitfor all
> set num_frames [molinfo top get numframes]
> set kk [expr $num_frames - 1]
> set a [atomselect top "protein and backbone and noh"]
> set c [atomselect top "protein and backbone and noh" frame $kk]
> for {set i 0} {$i<$num_frames} {incr i} {
> $a frame $i
> $a move [measure fit $a $c]
> }
> set outfile [open "rmsf_CAxx.dat" "w"]
> puts $outfile "Residue \t RMSF"
> for {set i 0} {$i < [$a num] } {incr i} {
> set rmsf [measure rmsf $a first 1 last $kk step 10]
> puts $outfile "[expr {$i+1}] \t [lindex $rmsf $i]"
> }
> close $outfile
>
>
>
> Regards,
> Dr.Mi
>
>
> On Tue, Dec 29, 2020 at 8:44 AM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
> Dear Dr. Mi,
> I think it is important to be clear about what is being counted as a
> 'residue' in each case. NAMD/VMD are probably counting all residues
> including ions/water when you look in the TCL window. PyMol is probably
> just counting protein residues. To understand your plot of '902 residues'
> in the RMSF, we need to know, what atom selection did you use for this
> calculation, and for that matter, how did you run it?
> Best,
> Peter
>
> On Thu, Dec 24, 2020 at 3:03 PM Mi Yang <drmiyang2019_at_gmail.com> wrote:
>
> Dear Colleagues,
> I have calculated RMSF using NAMD/VMD and got a plot of 902 residues vs
> distance
> But when I look the same protein in PyMol or other visualizer, its shows
> to me from 6 to 112 in sequence mood.
> A quick look into the TCL window show about 5760 residues
>
> Info) Analyzing structure ..
>
> Info) Atoms: 20107
>
> Info) Bonds: 14608
>
> Info) Angles: 11928 Dihedrals: 9360 Impropers: 587 Cross-terms: 221
>
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
>
> Info) Residues: 5760
>
> Info) Waters: 5534
>
> Info) Segments: 5
>
> Info) Fragments: 5537 Protein: 2 Nucleic: 0
>
>
> Any suggestion please because I want to see RMSF highest value for what
> residue?
>
>
> I already checked the NAMD tutorial guide but did not get an answer....
>
>
> Many thanks in advance!
>
>
> Dr.Mi
>
>
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