Hi James,
I think there is no way to force AutoBuild to build a full sequence when
there is no density.
All the best,
Tom T
On Tue, Apr 1, 2025 at 10:26 AM James Holton
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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-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010