[phenixbb] map to model - DNA model building

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Tue Aug 4 04:53:39 PDT 2020

Hi Manoj,

At a resolution of 3.3 A map_to_model is supposed to be able to build
regular DNA structures reasonably well, so it is worth trying a few things
to see if it can work better.

If you want only the DNA to be built by map_to_model then you do need to
tell map_to_model the solvent_content:
Usually it figures this out from the sequence file, but yours will only
represent a part of the model so you should specify it directly.  This
could have an effect but perhaps not huge.

Another thing to try is to cut out the density for a part of your DNA
chains and just work with that.  Map_to_model can work with a part of a map
just fine.  So try this:  find your best double-stranded DNA regular helix
and cut it out with map_box to make a small map. Now try to build with that
map.  If it doesn't work, you can send me this small map and I'll have a
look.  If it does work, you can make a few overlapping boxes and build up
overlapping parts of the molecule. Then you can combine them all with
phenix.combine_models and a map that covers all of them.

Let me know if these things don't help!

All the best,
Tom T

On Tue, Aug 4, 2020 at 3:19 AM Manoj saxena <mks131 at gmail.com> wrote:

>     Hello,
>     I am trying to fit a cryo-EM map of a DNA protein complex (3.3 A)
> using the
>     map to model
>     in Phenix,  with a DNA sequence input in fasta format and
> the
>     map as a .ccp4 file.
>     However the output  model fitted in the map I am getting is many
> fragmented
>     PDB files and only one chain of DNA.
>     What is the best way to get a higher fraction of the DNA model fitted
> into
>     the map, can I switch off the segmentation of map and get both strands
>     fitted into the map. Or the only option is to manually build?
>     Thanks for your help
>     Regards
>     Manoj Saxena
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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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