[phenixbb] Re: for autobuild full sequence?

1 Apr 2025

      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  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 
    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
_______________________________________________
    phenixbb mailing list [email protected]
    To unsubscribe send an email [email protected]
    Unsubscribe: phenixbb-leave@%(host_name)s
-- 
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