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

11 Dec 2015

      Hi Pavel,

Thank you very much for quick reply.
...
...
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!
This is caused because selection of the miller array is not right.

http://sourceforge.net/p/cctbx/code/22916/tree/trunk/mmtbx/command_line/map_...

should be something like this:

    found = False
    for ma in miller_arrays:
      if(ma.info().labels[0].lower() == params.label.lower()):
        found = True
        break
    if not found:
      raise Sorry("Specified label not found.")

Best regards,

Takanori Nakane

On Fri, 11 Dec 2015 09:51:27 -0800 Pavel Afonine  wrote:
...
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 >, 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

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

Takanori nakane