Yes, I tried this, and found that the disordered N terminus was
stabbing deep into the heart of a symmetry mate. phenix.refine was
not happy about this, and Amber went positively ballistic (so to
speak).
I suppose I could start with some kind of "pre-exploded" unit cell
where all the ASUs are far apart and then gradually try to bring
them together, but that seems like a lot of work.
On 4/1/2025 1:26 PM, Tom Terwilliger
wrote:
Hi James,
You could try this:
1. Get your best model, including only residues assigned to
sequence, with AutoBuild or whatever
2. Run AlphaFold (for example from the Phenix GUI where
this is easy) supplying the full sequence and supplying your
partially-built model. The resulting model should look mostly
like the one you supplied, with plausible connections for the
gaps.
All the best,
Tom T
On Tue, Apr 1, 2025 at 2:23 PM
James Holton <[email protected]>
wrote:
Yes, but I don't want it to clash with other molecules
in the unit cell, including itself.
When I was an undergrad, Steve Mayo called this an
"amorphous builder". Trivial in concept, but you need to do
a "bump check" after adding each atom, and then have a plan
for what to do if you hit a bump.
Make sense?
-James
On 4/1/2025 1:10 PM, Pavel Afonine wrote:
Hi James,
Are you just looking to string residues together in a line
from start to end according to your sequence? That’s a
quick 10-minute exercise using CCTBX, but I suspect that’s
not exactly what you need.
Pavel
On 4/1/25 12:28, Tom Terwilliger wrote:
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 <[email protected]>
wrote:
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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