From: Mi Yang (drmiyang2019_at_gmail.com)
Date: Wed Dec 30 2020 - 01:27:03 CST
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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