I think this is an excellent opportunity to combine MD calculations with your
structures to see what role(s) this flexible region may play in your structure.
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
I don't know anything about the practicalities of PDB2PQR but it
would seem to me that you have to calculate a potential for the molecule
with each conformation. Then you would say "This is the potential with
the A altloc and THIS is the potential with B". There will be no
individual molecule
how about mean square deviation of the rmsd of each c alpha？
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Smith Liu
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在2017年12月02日 22:48，Reza Khayat 写道：
Hi,
I'm analyzing the RMSD between 60 subunits of a virus. Can someone identify a
program that can generate a spread for the
Hi,
I'm analyzing the RMSD between 60 subunits of a virus. Can someone identify a
program that can generate a spread for the RMSD between equivalent C-alpha
atoms? For example, the C-alpha atom for amino acid 39 may have RMSD values
from 0.1 to 1.5. Coot does a nice job of automatically
To add to the discussion, could I raise a relevant question about
generating ESP (Apologies to Jiri if this distracts too much from your
initial thread).
In our structure in hand, the density for two conformations of the side
chain are clearly seen and they could be modeled. This brings a bit of
