Hi James,

Yes, that makes sense, and it’s what I suspected. Creating a string of residues that matches your sequence is, as I mentioned, a ten-minute exercise in CCTBX. However, ensuring that it folds within the allowed volume, avoids self-clashes, and meets other geometric quality metrics is a more complex challenge—but not impossible.

My approach would be to create a map where all voxels occupied by existing atoms have negative values. Then, assuming the start and end points of your chain are known, I’d generate a rough path through non-negative voxels. From there, a round of real-space simulated annealing could refine the structure.

But that’s starting to sound like a full project now!

Pavel

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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--

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

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