[phenixbb] Average maps (*not* NCS averaging)

Stephen Graham scg34 at cam.ac.uk
Fri Mar 11 03:29:14 PST 2011

Dear all,

Thanks for the many responses.

I can easily generate superposed maps using phenix.superpose_maps.
Unfortunately this doesn't create maps with the same origin and
extents, etc., thus neither COMAP nor any of the CCP4 tools I've found
will average them trivially (I was trying to be lazy and get around
having to get the maps onto the same sampling grid...).

Donnie: Can COOT average arbitrary maps?  I could not find that in the
online documentation (just NCS averaging).

Frank: Agreed when you have a high res 'good' structure and a low res
'bad' one.  I have two high res data sets where a loop is modelled
(incorrectly) in both and am trying to clean up the density for
building, rather than restrain a wayward structure to a known ideal

Pavel: Unfortunately your script dies with array bounds errors:
      else: data += ma.data()
  RuntimeError: scitbx array_family range error
Is this because it assumes the two mtz files have the same resolution
(i.e. len(ma) is the same for all)?

I was not fully aware of the caveats Fred mentioned - if histogram
matching is a must I'm probably better of doing this 'properly' using

Again, thanks for all the comments,


On 11 March 2011 08:14, Frank von Delft <frank.vondelft at sgc.ox.ac.uk> wrote:
> I'm not sure this is a particularly rigorous way to get "noisier bits" less
> noisy.  Surely the way to do it is to refine one model using the other model
> as restraints.  Both refmac and buster do it, (maybe phenix.refine too).
> Cheers
> phx
> On 10/03/2011 17:15, Stephen Graham wrote:
>> Hi there,
>> I'd like to average 2Fo-Fc maps from 2 (approximately) isomorphous
>> data sets (one with ligand, one without) to see whether I get better
>> density for some of the noisier bits of the structure.  I don't want
>> to do any kind of solvent flattening, histogram matching, cyclical
>> averaging, etc; I just want to sum the equivalent pixels and divide by
>> 2.
>> Is it possible to do this easily using any of the phenix tools?  It
>> seems like all the required plumbing is there with get_cc_mtz_mtz or
>> superpose_maps, but I can't find a phenix utility for averaging two
>> superposed maps.
>> Thanks,
>> Stephen

Dr Stephen Graham
1851 Research Fellow
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital, Hills Road
Cambridge, CB2 0XY, UK
Phone: +44 1223 762 638

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