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

[Yangqi Gu]

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 at 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 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
>
>

-- 

Yangqi Gu
Ph.D.
Yale University, West Campus
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