There are some issues which may be affecting some people using Coot with
PHENIX. If you try and use the two together in the wrong way, then you
may get unexpected results. (Problems hashed out with help from Dirk).
phenix.refine produces two different sets of output files. I quote from
the documentation:
At the end of refinement the program generates:
...
two maps: likelihood weighted mFo-DFc and 2mFo-DFc. These are
in ASCII X-PLOR format. A reflection file with map coefficients
is also generated for use in Coot or XtalView (e.g.
lysozyme_refine_001_map_coeffs.mtz);
There are some CNS maps, which may be used in conventional graphics
programs, and there is an MTZ file, which may be used in Coot or XtalView.
The difference is important. Coot and XtalView have a fundamentally
different concept of what a map is to other graphics programs. As a
result they require different information. Phenix.refine recognises this
and provides appropriate information for each type of program.
In the last year we incorporated the ability to read CNS files into
coot. As a result, some users have started reading the CNS map files
into coot instead of the MTZ file. Unfortunately, this does not always
work the way you would expect, because the map files has not been
generated with Coot in mind. This may lead to misleading sigma levels,
or, if the map is modified or masked in any way before giving it to
Coot, much more serious artifacts.
The solution is simple: When using Coot, use the MTZ file which the
phenix developers have provided for that purpose, *not* the CNS map
files. In addition to giving the right answers, there are some other
benefits:
- The MTZ is much smaller, in case you want to archive it.
- Using auto-open mtz, you get both maps at once, and the difference
map is automatically displayed as such, saving mouse clicks.
- The spacegroup and cell information are in the file, so it works
even if you don't open the PDB file first.
..
You can stop reading here, the rest is detail for those who are interested:
Coot and XtalView use a different representation of electron density, a
continuous crystal representation. Most other graphics programs use a
bounded box representation.
The continuous crystal representation means that the electron density is
everywhere, it is omnipresent. "If I scroll up to the heavens, density
is there; if I place my ligand in the depths, density is there. If I
drag over to the far side of the solvent, even there the density will
guide my fitting." (*)
To generate a continuous crystal representation, you need a complete and
consistent description of the electron density over the asymmetric unit
(any asymmetric unit - it doesn't matter where in space). The bounded
box representation need the electron density over the volume of the
molecule.
It is not always possible to get the asymmetric unit representation from
the bounded box representation, because in creating the bounded box some
information may have been lost. However, you can always get it from an
MTZ file, or from a map file on the condition that the map file is
appropriately bounded.
Kevin
(*) Psalm 139 v8-10
