[phenixbb] Fwd: [COOT] Using Coot with PHENIX

Stephen Graham stepheng at strubi.ox.ac.uk
Wed Jul 2 02:00:43 PDT 2008

Below is an email from Kevin Cowtan (posted on the COOT bb) that may
be of interest to people who use COOT for building.


---------- Forwarded message ----------
From: Kevin Cowtan <cowtan at ysbl.york.ac.uk>
Date: Jul 2, 2008 9:31 AM
Subject: [COOT] Using Coot with PHENIX
To: COOT at jiscmail.ac.uk

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.

 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

 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
  - 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.


 (*) Psalm 139 v8-10

Dr Stephen Graham
Nuffield Medical Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549

More information about the phenixbb mailing list