Hey all,

Don't worry, nothing is funny today.  I have a real question:

Is there a way to force phenix.autobuild to build in the entire
sequence?  As in: the full length of the actual molecule that is in the
crystal, such as what is supposed to go into SEQRES, regardless of
"visible" density?  I am trying to come up with a pipeline for prepping
MD simulations of protein crystals.  It seems proper to me that the
molecule being simulated should be the actual molecular species,
disordered bits an all.  However, we don't seem to have good technology
for building protein chains into "nothingness". Yes, I know Alphafold is
a thing, but it is rubbish at clashes in the context of a crystal.

I mean, I could write something, but does this tool already exist?

Cheers, and happy Tuesday,

-James Holton
MAD Scientist


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