[phenixbb] Using AutoBuild to Complete a Model

[Folmer Fredslund]

Dear Matthew,

You say you have 16 identical chains?
Is the electron density also identical between them?
How close are the NCS related copies?

I would choose to use Coots built-in NCS tools to copy the model from one
chain to the others. Takes a few seconds tops, and then normal refinement
should take care of the rest.

See e.g. here
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Applying-NCS-Edits




Unless of course all these N-terminal residues are rather different, then
it's a different story, but not quite sure about it from your description.

Hope this helps

Folmer




tir. 17. aug. 2021 08.16 skrev Whitley, Matthew J <mjw100 at pitt.edu>:

> Hello all,
>
>
>
> I have a very large protein with 16 copies in the asymmetric unit (nearly
> 15,000 total residues).  Upon initial model building, ~30 residues at the
> N-terminus of each identical chain were not built.  After building the
> reliable parts of the model and filling in other gaps and then refining
> that partial (but nearly complete) model, the N-terminal density has now
> improved to the degree that I can manually build a number of the missing
> residues in Coot.  However, that means manually building the same series of
> residues over and over for each of the 16 identical chains.  Is there a way
> to get AutoBuild to add these N-terminal residues for me to spare me the
> tedium of repetitive manual building?
>
>
>
> What I’ve gleaned from the documentation so far:
>
>
>
> From the phenix.fit_loops documentation, it seems like that tool only
> works for filling in chain breaks, i.e. there is already modeled protein at
> each end of the missing region.  That’s not the case for me because I’m
> trying to work backward toward the N-terminus.
>
>
>
> If I am reading the phenix.autobuild documention correctly, it sounds like
> there are two modes:
>
> (i)                 Standard mode - rebuild the whole protein from
> scratch, which does give the possibility of adding my N-terminal residues.
> However, I don’t want my nearly complete existing model to be rebuilt, I
> just want AutoBuild to try to add the missing N-terminal sequence to the
> existing model.
>
> (ii)              Rebuild-in-place, which rebuilds the current model but
> doesn’t add or subtract any atoms.  So that sounds like it’s not what I’m
> looking for because it won’t add the N-terminal sequence AND it rebuilds
> the existing model, which I want to keep exactly as is.
>
>
>
> Is there some series of options in AutoBuild that will allow me to just
> add missing residues (provided in the sequence file) but keep all the other
> currently existing residue in the input model exactly as they are?
>
>
>
> Happy to hear any advice you can give.
>
>
>
> Thanks,
>
> Matthew
>
>
>
> ---
>
> *Matthew J. Whitley, Ph.D.*
>
> Research Instructor
>
> Department of Pharmacology & Chemical Biology
>
> University of Pittsburgh School of Medicine
>
>
>
>
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