Hi, look for " def combine_maps" here: http://cci.lbl.gov/~afonine/mssa2/run.py that does it what you want. It reads in all files with map coefficients, averages them, and outputs averaged map coefficients. Since Fourier transformation is a linear operation, averaging map coefficients is equivalent to averaging actual maps. In 5 minutes I can turn this script into something like phenix.average_map_coefficients map_coeff1 map_coeff2.mtz labels=" 2FOFCWT" Do we need this tool? Tom, how much of non-isomorphism we should allow before the above tool stops? Pavel. On 3/10/11 9:49 AM, Tom Terwilliger wrote:

Hi Stephen, I don't know of any phenix tools that will average two maps, though you are right that everything is there to do it quite easily. -Tom

On Mar 10, 2011, at 10:15 AM, 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] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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On 20:41 Thu 10 Mar , Pavel Afonine wrote:

Donnie,

Coot is not a part of PHENIX and is not distributed with PHENIX. PHENIX can use Coot if it is available (installed separately by the user).

Thanks for the clarification. I guess if I had said "integrated with phenix," it would have been right. The important part of the answer remains.. -- Thanks, Donnie Donald S. Berkholz, Ph.D. Research Fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Medical Sciences 2-66 Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 office: 507-538-6924 cell: 612-991-1321

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 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 _______________________________________________ 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.

Yes, I even pointed you to the relevant menu entries. I've previously used this to average maps from crystals in two different space groups.

Ah - so there is! My bad. This is the perfect quick-and-dirty solution I was looking for...it even gives some (subjectively) slightly more interpretable density. Now off to tackle this bad loop... 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