[phenixbb] map to model - DNA model building
tterwilliger at newmexicoconsortium.org
Tue Aug 4 06:52:11 PDT 2020
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:
so that it knows what to do with this piece of the map.
All the best,
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:
>> I am trying to fit a cryo-EM map of a DNA protein complex (3.3 A)
>> using the
>> map to model
>> in Phenix 18.104.22.16874, with a DNA sequence input in fasta format and
>> map as a .ccp4 file.
>> However the output model fitted in the map I am getting is many
>> PDB files and only one chain of DNA.
>> What is the best way to get a higher fraction of the DNA model fitted
>> 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
>> Manoj Saxena
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> Unsubscribe: phenixbb-leave at phenix-online.org
> 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
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