[phenixbb] Educative Tool Idea

Pavel Afonine pafonine at lbl.gov
Tue Sep 13 15:52:28 PDT 2011

Hi Yuri,


does something similar. It takes a PDB file with a model, and outputs an 
MTZ file with generated Fobs. It tries to include as many things as 
reasonably possible:

- crystal anisotropy,
- bulk-solvent;
- local model model disorder;
- global model vibrations using TLS,
- adds H if missing,
... and more.

You can take this fake data and refine model against it to R=0% (if you 
manage to come up with the appropriate refinement strategy).

Not sure what it is good for, except for developers.

Reflection file viewer is available from PHENIX GUI - it allowed you to 
see reciprocal space in 2 or 3D. See Nat's article "A lightweight, 
versatile framework for visualizing reciprocal-space data" here

There are more tools in PHENIX that more or less fit into description of 
what you want, I guess.


On 9/13/11 3:37 PM, Yuri wrote:
> Hello Developers,
> This may be a silly idea after all, nonetheless:
> Would it be possible (worhtwhile) to have a tool that lets the user 
> input a molecule of a certain type (probably rather
> small size, i.e, an amino acid or cofactor), and then input a space 
> group.
> Phenix could then generate a relection file that would be displayed 
> using either data2d or 3d viewer.
> Obviously there are many other factors to be considered but just an 
> idea...

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