Hi Harry,
The superpose/overlay of all the structures in PyMol should inform you the
rigid part of the protein as well as the flexible part. The rigid part would
have very low backbone RMSD or overlay tightly and the flexible part (loops,
N-term and C-term etc.) would not superpose tightly. If you check literature,
the dynamics of the protein may have been studied through NMR relaxation.
Smita
On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB
<0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
Hi
Given that there are plenty of people on this BB who are structural biologists
rather than “just” crystallographers, I thought someone here might be able to
help.
If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures
that fit the NOEs, is there a tool available that will give me some idea about
the bits of the structure that do not vary much (“rigid”) and the bits that are
all over the place (“flexible”)?
Would superpose or gesamt be a good tool for this? Ideally I’d like something
that could add a figure to the B columns in a PDB file so I could see something
in QTMG (or PyMol if forced…) or do other useful things with the information.
Harry
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