Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF

From: varun dewaker (
Date: Wed Dec 30 2020 - 01:45:49 CST

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

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  On Wed, Dec 30, 2020 at 12:59 PM, Mi Yang<> 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 psfmol addfile solvate.pdb type pdbmol addfile output.dcd type dcd first 0 last -1 step 5 waitfor allset 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


On Tue, Dec 29, 2020 at 8:44 AM Peter Freddolino <> 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,

On Thu, Dec 24, 2020 at 3:03 PM Mi Yang <> wrote:

Dear Colleagues,I have calculated RMSF using NAMD/VMD and got a plot of 902 residues vs distanceBut 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...------=_Part_3452212_2053070363.1609314349740--

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