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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">Subject:
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<td>Re: [cctbxbb] phenix.map_value_at_point does not work
with ccp4 maps</td>
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">Date: </th>
<td>Fri, 11 Dec 2015 09:51:27 -0800</td>
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">From: </th>
<td>Pavel Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a></td>
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">To: </th>
<td>cctbx mailing list <a class="moz-txt-link-rfc2396E" href="mailto:cctbxbb@phenix-online.org"><cctbxbb@phenix-online.org></a>,
<a class="moz-txt-link-abbreviated" href="mailto:takanori.nakane@bs.s.u-tokyo.ac.jp">takanori.nakane@bs.s.u-tokyo.ac.jp</a></td>
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<pre>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.
> <a class="moz-txt-link-freetext" href="http://phenix-online.org/pipermail/cctbxbb/2015-September/001155.html">http://phenix-online.org/pipermail/cctbxbb/2015-September/001155.html</a>
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
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