From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Dec 28 2020 - 23:44:34 CST
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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