Failure in phenix.map_box when working with map files....

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Ezra Peisach

7 Sep 2015 7 Sep '15

2:59 p.m.

Has anyone observed a failure of phenix.map_box when working with map files? When working with a structure factor file with map coefficients, it works fine. When a map file is used - the following occurs: Traceback (most recent call last): File "/local/scratch/CCTBX/cctbx_build/../cctbx_sources/mmtbx/command_line/map_box.py", line 194, in <module> run(args=sys.argv[1:]) File "/local/scratch/CCTBX/cctbx_build/../cctbx_sources/mmtbx/command_line/map_box.py", line 158, in run selection = selection) File "/local/scratch/CCTBX/cctbx_sources/mmtbx/utils/__init__.py", line 2938, in __init__ self.map_box = maptbx.copy(map_data, gridding_first, gridding_last) Boost.Python.ArgumentError: Python argument types in cctbx_maptbx_ext.copy(double, list, list) did not match C++ signature: copy(scitbx::af::const_ref > map_unit_cell, scitbx::af::tiny first, scitbx::af::tiny last) copy(scitbx::af::const_ref > map_unit_cell, scitbx::af::tiny first, scitbx::af::tiny last) copy(scitbx::af::const_ref > > map, scitbx::af::flex_grid > result_grid) copy(scitbx::af::const_ref > > map, scitbx::af::flex_grid > result_grid) Any suggestions? The map_data is the same format in the call....

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Pavel Afonine

7 Sep 7 Sep

3:31 p.m.

Hi Ezra, could you please send me the file that generated this crash? Thanks, Pavel On 9/7/15 07:59, Ezra Peisach wrote:

...

Has anyone observed a failure of phenix.map_box when working with map files? When working with a structure factor file with map coefficients, it works fine.

When a map file is used - the following occurs:

Traceback (most recent call last): File "/local/scratch/CCTBX/cctbx_build/../cctbx_sources/mmtbx/command_line/map_box.py", line 194, in <module> run(args=sys.argv[1:]) File "/local/scratch/CCTBX/cctbx_build/../cctbx_sources/mmtbx/command_line/map_box.py", line 158, in run selection = selection) File "/local/scratch/CCTBX/cctbx_sources/mmtbx/utils/__init__.py", line 2938, in __init__ self.map_box = maptbx.copy(map_data, gridding_first, gridding_last) Boost.Python.ArgumentError: Python argument types in cctbx_maptbx_ext.copy(double, list, list) did not match C++ signature: copy(scitbx::af::const_ref > map_unit_cell, scitbx::af::tiny first, scitbx::af::tiny last) copy(scitbx::af::const_ref > map_unit_cell, scitbx::af::tiny first, scitbx::af::tiny last) copy(scitbx::af::const_ref > > map, scitbx::af::flex_grid > result_grid) copy(scitbx::af::const_ref > > map, scitbx::af::flex_grid > result_grid)

Any suggestions?

The map_data is the same format in the call.... _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Takanori Nakane

11 Dec 11 Dec

9:09 a.m.

New subject: phenix.map_value_at_point does not work with ccp4 maps

Dear all, I encountered an error with phenix.map_value_at_point. It does not work when ccp4 maps are provided. It works fine when an mtz file with map coefficients is provided. Probably this is related to the bug reported last September. http://phenix-online.org/pipermail/cctbxbb/2015-September/001155.html 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. 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! Best regards, Takanori Nakane

Pavel Afonine

5:51 p.m.

New subject: phenix.map_value_at_point does not work with ccp4 maps

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

Pavel Afonine

5:52 p.m.

New subject: Fwd: Re: phenix.map_value_at_point does not work with ccp4 maps

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 To: cctbx mailing list , [email protected] 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

Takanori nakane

12 Dec 12 Dec

1:25 a.m.

New subject: phenix.map_value_at_point does not work with ccp4 maps

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

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Ezra Peisach
Pavel Afonine
Takanori nakane
Takanori Nakane