[Chimera-users] Dock PDB into low resolution EM map.

[Jordan Benjamin]

I spent some time doing this recently. Chimera is a wonderful tool for
this purpose. There is a very helpful (and short!) tutorial you should
work through:
http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/07-VolumeData/tutorial/chaperonin.html

There is a sort of local search tool for fitting models to density,
although I think you need ot have pretty good data for it to work.


On 6/11/06, Puey Ounjai <pounjai at gmail.com> wrote:
>
> Dear all,
>
> I am trying to dock atomic coordinate of a protein derived from 3D X-ray
> crystal (PDB format) into lower resolution (about 20-25 A resolution) EM map
> (BRIX, XPLOR ASCII or SITUS format) from 2D crystal.
>
> 1. Does Chimera have this kind of fitting tool (PDB to volume) or I have to
> fit the coordinate by hand? If chimera can do this task, Which command
> should I use?
> 2. Does Chimera have any statistical evaluation for manual fitting?
> 3. How can you evaluate the % matching of 2 models in Chimera?
>
> Best regards,
> Puey Ounjai
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