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 < [email protected]> 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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010

-- Yangqi Gu Ph.D. Yale University, West Campus