[phenixbb] Help with AutoBuild

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Sat Dec 15 20:04:35 PST 2018

Hi Partha,

You can turn off the ncs with "find_ncs=False" in either GUI or

It is harder to only work on part of the molecule. If you can use
"rebuild_in_place" (not adding/deleting residues) then you can specify a
range of residues/chains to rebuild.  However if you are adding/deleting
with rebuild_in_place=False, you are stuck.   One solution is rebuild all
of it, and then recombine with the good (fixed) molecule using
phenix.combine_models which should keep (most of ) your good chain.

All the best,
Tom T

On Sat, Dec 15, 2018 at 4:55 PM Parthasarathy Sampathkumar <
spartha2 at gmail.com> wrote:

> Dear All,
> These days my research often involves structure determination of
> the Antigen:Fab complexes, wherein the antigen structure is already known.
> Given this: (1). I would like to run AutoBuild in such a way that the
> program does not to touch antigen model, but only Re-builds only the Fab
> molecule; and (2). in some cases, due to structural-symmetry within the
> variable and constant domains of heavy- and light- chains, AutoBuild is
> searching and applying NCS operator while it is not present, and would like
> to avoid the same.
> How could these be done either in GUI or in command-line?!!
> Many Thanks in advance,
> Best Wishes
> Partha
> PS: Of course, when the data is at "high-enough resolution", I build Fab
> model manually after MR and Refinement. But, in the above case, resolution
> is only 3-ish angstrom.
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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: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0033
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