Hello Stephen-
I may be wrong but it seems like you are just doing averaging between two crystals. If so can you just use MAVE from the Uppsala software package RAVE? I'm pretty sure i did this with help from MAPMAN(to help with the issues of extent, etc). I'll look for a script when I get to work.
- Todd
-----Original Message-----
From: [email protected] on behalf of Stephen Graham
Sent: Fri 3/11/2011 5:29 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Average maps (*not* NCS averaging)
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
model.
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
resolve/dmmulti/etc.
Again, thanks for all the comments,
Stephen
On 11 March 2011 08:14, Frank von Delft
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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb This email was scanned with Mcafee's Anti-Virus appliance, but this is no guarantee that no virus exists. You are asked to make sure you have virus protection and that it is up to date.