[cctbxbb] Fwd: Re: phenix.map_value_at_point does not work with ccp4 maps

[Pavel Afonine]

Sorry if you get it twice...


-------- Forwarded Message --------
Subject: 	Re: [cctbxbb] phenix.map_value_at_point does not work with 
ccp4 maps
Date: 	Fri, 11 Dec 2015 09:51:27 -0800
From: 	Pavel Afonine <pafonine at lbl.gov>
To: 	cctbx mailing list <cctbxbb at phenix-online.org>, 
takanori.nakane at bs.s.u-tokyo.ac.jp



Hi Takanori,

> I encountered an error with phenix.map_value_at_point.
> It does not work when ccp4 maps are provided.

indeed! At present it only works with MTZ files. It is a trivial effort
to extend it to accepting the map too. I will do it in a day or two
(writing from airport..).

> It works fine
> when an mtz file with map coefficients is provided.

As expected.

> Probably this is related to the bug reported last September.
> http://phenix-online.org/pipermail/cctbxbb/2015-September/001155.html

Yes, maps are not expected in input!

> It also has a problem that when there are multiple columns in an mtz
> file and the specified label does not match any of them, the
> last column is used without warning.

Hm.. this is not good, I will have a look!

> phenix.fetch_pdb 3eml
> phenix.fetch_pdb -x 3eml
> phenix.maps 3eml.pdb 3eml-sf.cif
>
> # Just to use the latest svn version
> cctbx.python
> ~/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py
> point="1.0 2.0 3.0" 3eml_2mFo-DFc_map.ccp4
>
> Default params::
>
>   label = None
>   point = None
>   resolution_factor = 0.25
>   scale = *sigma volume
>   resolution = None
>   low_resolution = None
>
> Map values at specified points:
> Traceback (most recent call last):
>   File
> "/mnt/wd_storage/nakane/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py",
> line 162, in <module>
>     run(sys.argv[1:])
>   File
> "/mnt/wd_storage/nakane/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py",
> line 146, in run
>     "%10.3f"%map_3d.eight_point_interpolation(point_frac)).strip()
> Boost.Python.ArgumentError: Python argument types in
>     cctbx_maptbx_ext.eight_point_interpolation(double, tuple)
> did not match C++ signature:
>     eight_point_interpolation(scitbx::af::const_ref<double,
> scitbx::af::c_grid_padded<3ul, unsigned long> >, scitbx::vec3<double>)
>
> cctbx.python
> ~/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py
> 3eml_map_coeffs.mtz point="1.0 2.0 3.0" label="2FOFCWT" # This works fine
>
> cctbx.python
> ~/prog/dials/modules/cctbx_project/mmtbx/command_line/map_value_at_point.py
> 3eml_map_coeffs.mtz point="1.0 2.0 3.0" label="WRONG_LABEL" # but this
> also proceeds!

Thanks! I will investigate and get back to you! This is very valuable
information.

All the best,
Pavel



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20151211/9a44bcae/attachment.htm>