[phenixbb] Looking at omit maps in coot

[Nathaniel Echols]

On Fri, May 14, 2010 at 6:45 PM, xaravich ivan <xaravich.ivan at gmail.com>wrote:

> Its the latest version I downloaded less than a week back. It is in Mac OS
> X. I am using GUI. Basically I have made most of the model and as it was
> from Molecular Replacement it still has that high R free and I am sure that
> parts of the model has that bias and does not fit niceley. I deleted those
> regions and used SA_omit map in phenix GUI. It made a composite omit map by
> default. and it has made those number of regions of pdb and mtz files.
>

FYI, if you are generating a composite omit map, you do not need to delete
anything first.  If you just want to look at a specific region, there are
much faster ways to do this:

1. Specify the region to omit "Omit map options->Omit region specification",
either using a PDB file containing the atoms to leave out, or an atom
selection.
or
2. delete the region manually, then run phenix.refine with simulated
annealing for a couple of macrocycles, and look at those maps.

As long as you have simulated annealing turned on (always a good idea for
omit maps), these are approximately equivalent.  The composite omit
procedure basically does (2) for every region of the model, then stitches
the maps around those regions back together, so it will take ~20x longer to
run.

The coot is distinctly indicating that it could not open the map/mtz. even
> when I try to open from phenix or separately from command line.
>

That sounds bad.  Could you please send me (not the list!) the final MTZ
file?

thanks,
Nat
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