Hello:
I am trying to see the effect of side-chain fluctuation on molecular
permeation through a transmembrane protein channel.
The idea is create a pdb file with a column of B-values related to the RMSF
values of the MD trajectory.
What I tried was to set the B-values of all heavy atom main-chain atoms to
1.0. Then all the B side-chain values were set equal to the RMSF value
from the trajectory, using the correct formula relating RMSF fluctuation to
B-value.
But, the above method blows up in pymol when trying to use the Action --->
Preset ---> b factor putty option. I think this is probably due to the
fact that all main-chain atoms are equal to 1, and the algorithm cannot
handle this.
Can someone please provide me with a way to clearly see the fluctuation of
sid-chain atoms in the present of the main-chain atoms?
Thanks so much.
Regards,
Angelo
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