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

From: Mi Yang (
Date: Thu Dec 24 2020 - 13:02:23 CST

Dear Colleagues,
I have calculated RMSF using NAMD/VMD and got a plot of 902 residues vs
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

I already checked the NAMD tutorial guide but did not get an answer....

Many thanks in advance!


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