From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Dec 30 2020 - 12:52:19 CST
Are you trying to do RMSFs for the backbone atoms (which includes several
atoms per residue) or for the alpha carbons? The comments and variable
names suggest the latter, but your code (when you use 'backbone' as the
atom selection) does the former.Best,
Peter
On Wed, Dec 30, 2020 at 12:17 PM Mi Yang <drmiyang2019_at_gmail.com> wrote:
> 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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