From: Mi Yang (drmiyang2019_at_gmail.com)
Date: Wed Dec 30 2020 - 11:17:23 CST
Dear Varun,
I have found the solution: its ok to use residue numbers.
Here is RSMF with "protein and backbone and noh"
With Residue numbers from 18-116 (total: 99)
On Wed, Dec 30, 2020 at 5:04 PM Mi Yang <drmiyang2019_at_gmail.com> wrote:
> 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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