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 <jmholton@lbl.gov> 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 <jmholton@lbl.gov>
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?