[Chimera-users] Looking at docked data with the receptor shows as surface

[Jonathan Y Wang]

To whom it may concern,

Hi! I recently docked a ligand onto a receptor using the AutodockVina tool
and when I opened the data the ligand seemed to be placed in the middle of
the trimer. I showed the receptor as surface and it seems as if the ligand
is too big to fit inside any of the holes surrounding the trimer, but
somehow it has placed itself inside. I additionally opened it using PyMol
to double check the file, but it also seems too small to fit inside any of
the holes.

My inquiry is this: Does AutodockVina take into account surface projections
when performing docking?

Thank you so much for your time,
Jonathan Wang
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