Re: [phenixbb] map to model - DNA model building

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 < [email protected]> 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 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 _______________________________________________ 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

-- 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