[phenixbb] Building DNA into the cryo-EM map density

[Tom Terwilliger]

Hi Yangqi,

You can try using

   phenix.map_to_model my_map.ccp4 seq.dat nproc=8 resolution=3

or something like that.  You might first want to cut out the DNA part of
the map with phenix.map_box.  Your seq.dat can in this case be just the DNA
sequence. It will usually know it is DNA from the sequence but you could
also say "chain_type=DNA"

Let us know if that doesn't work!
All the best,
Tom T

On Tue, Jun 14, 2022 at 10:13 AM Yangqi Gu <yangqi.gu at yale.edu> wrote:

> Dear PHENIX users and developers,
> I am currently building a model for a cryo-EM map of a helical complex. I
> could build the protein easily into the map. However, the map also contains
> a long chain of DNA density, I am wondering what could be the best way to
> build this DNA model? I have no previous experience building models with a
> DNA complex, therefore any suggestion would be helpful!
> Best.
> Yangqi
>
> --
>
> Yangqi Gu
> Ph.D.
> Yale University, West Campus
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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: 505-431-0010
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