[phenixbb] map to model - DNA model building

Tom Terwilliger tterwilliger at newmexicoconsortium.org
Tue Aug 4 06:52:11 PDT 2020


Hi Manoj,
I forgot to mention...if you cut out just a small piece of a map with
map_box and run map_to_model, be sure to specify:
   segment=False
   asymmetric_map=True
so that it knows what to do with this piece of the map.
All the best,
Tom T

On Tue, Aug 4, 2020 at 5:53 AM Tom Terwilliger <
tterwilliger at newmexicoconsortium.org> wrote:

> 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 1.18.2.3874,  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
>
>

-- 
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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