Hi Tom,
Sorry for a late reply. I tried by first extracting one strand of DNA density in Chimera and then I used the  phenix.map_to_model my_map.ccp4 seq.dat nproc=8 resolution=4 to build the DNA, but it did not work. Nothing was built. I am wondering if it is because of the phenix.map_box command you were mentioning? Could you give me a bit more advice on how to proceed? Thank you!
Best,
Yangqi

On Tue, Jun 14, 2022 at 12:54 PM Tom Terwilliger <tterwilliger@newmexicoconsortium.org> wrote:
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@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
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--

Yangqi Gu
Ph.D.
Yale University, West Campus