[chimera-dev] Save PDB and Map before fitting

[Pablo Solar Rodríguez]

Hello Eric,

The 1,2, 3 and 4 points are correct. In 5, there is something wrong; we
don't open the old pdb, it's already open from the start.

We tried to apply the transform:

pdb_model.openState.xform * map.openState.xform.inverse()

Without succes results. Do we have to premultiply pdb xform with map
inverse xform?

When we  move the pdb to the fittings positions, we do something similar to
what "Transform coordinates" in the "Movement" menu does (
http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/
libs/MoleculeTransform/gui.py):

- Reset: get the applied_xform inverse from the old pdb, transform atom
coordinates with pdb atoms and this xform and record xform*. (similar to
"Transform coordinates" Reset)
- Move to center of mass: get euler xform with (0, 0, 0) euler angles and
old pdb center coordinates, transform atom coordinates with old pdb atoms
and this xform and record xform*.
- For each solution, get euler xform with euler angles of the solution and
solution fitting coordinates, transform atom coordinates with old pdb atoms
and this xform and record xform*
- *Record xform is similar to "Transform coordinates" record xform.

Maybe we have wrong concepts at the time we are trying to move the molecule
in this advanced situation (remember that the basic situation without
moving is working fine)

Thank you so much for your help. Kind regards!

2017-05-03 0:51 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:

>
> On May 2, 2017, at 3:50 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> so to get the old PDB to the fitted position, you would need to replace
> its openState.xform with:
>
> fitted_xform * pdb_model_when_saved.openState.xform *
> map_when_saved.openState.xform
>
>
> forgot to add the “.inverse()” to the end of that…
>
> —Eric
>
>
>


-- 

*Pablo Solar Rodríguez*

*pablosolar.r at gmail.com <pablosolar.r at gmail.com>*
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