[phenixbb] Re: for autobuild full sequence?

1 Apr 2025

      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  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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