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Wrong conversion from CCP4 to DX #76

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nezix opened this issue Dec 5, 2019 · 5 comments · Fixed by #100
Closed

Wrong conversion from CCP4 to DX #76

nezix opened this issue Dec 5, 2019 · 5 comments · Fixed by #100
Labels
defect format-MRC MRC/CCP4 file format format-OpenDX OpenDX file format

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@nezix
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nezix commented Dec 5, 2019 •
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Importing a CCP4 map to convert it to a DX file outputs an inverted DX file.

from gridData import Grid
g = Grid("1cbs.ccp4")
g.export("1cbs.dx")

When displaying the DX file in Pymol or VMD, the molecule does not fit in the iso-surface

Level 1 of the exported DX file in Pymol:
image

Level 1 of the CCP4 file in Pymol:
image

Did I miss something ?
@orbeckst
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That looks wrong... do you have an example file that you can add to the issue or link?

@nezix
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nezix commented Feb 19, 2020

You can find the ccp4 file here https://www.ebi.ac.uk/pdbe/coordinates/files/1cbs.ccp4

@orbeckst orbeckst mentioned this issue Feb 19, 2020
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@orbeckst
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I can confirm this bug.

Furthermore, the DX density appears to be stretched (see Chimera image, contours at 0.362)

  • gray: 1cbs.ccp4
  • yellow: DX file from gridDataFormats
  • licorice (barely visible) 1cbs.pdb

1cbs_ccp4_dx

@orbeckst orbeckst mentioned this issue Sep 10, 2021
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@orbeckst orbeckst added format-MRC MRC/CCP4 file format format-OpenDX OpenDX file format labels Sep 10, 2021
@orbeckst
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Do we know if the problem is with

  • CCP4 reading
  • CCP4 interpretation (conversion to Grid)
  • something else (probably not DX writing because that's been used widely)

@orbeckst
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PR #100 does not fix this bug. In ChimeraX loading the densities gives

  • CCP4 file: 81 x 70 x 96
  • dx file: 70 x 81 x 96

Clearly there's something wrong in how gridData interprets the data in some(?) CCP4 files.

@orbeckst orbeckst mentioned this issue Jan 11, 2022
Merged
orbeckst added a commit that referenced this issue Feb 19, 2022
@orbeckst
correct orientation of axes from MRC file
933cf9d 
- mrcfile only reshapes the data to nz,ny,nx but does not take
  the mapc, mapr, maps into account. For gridData we need to
  do the coordinate system reorientation after transposing the
  mrcfile.data to nx, ny, nz.
- add test (using CCP4_1JZV from the test data which contains
  mapc, mapr, maps = 2, 1, 3
- manually checked 1cbs.ccp4 from issue #76 (also a 2, 1, 3)
  and orientation is now correct but there is still an offset error
  that needs to be fixed
orbeckst added a commit that referenced this issue Feb 19, 2022
@orbeckst
correctly reorient and center coordinates from MRC
a6b2519 
- fix #76
- add tests
@orbeckst orbeckst linked a pull request Feb 19, 2022 that will close this issue
use mrcfile library for MRC/CCP4 file parsing #100
Merged
orbeckst added a commit that referenced this issue Feb 20, 2022
@orbeckst @tluchko
reorder MRC data according to mapc,mapr,maps
508ab8b 
- mrcfile stores data in z,y,x format: we use the information
  of the axis orientation in mapc, mapr. maps to orient the
  data in the GridDataFormats x,y,z coordinate system
- correctly reorient and center coordinates from MRC
  - fix #76
  - add tests
- mrcfile only reshapes the data to nz,ny,nx but does not take
  the mapc, mapr, maps into account. For gridData we need to
  do the coordinate system reorientation after transposing the
  mrcfile.data to nx, ny, nz.
- add test (using CCP4_1JZV from the test data which contains
  mapc, mapr, maps = 2, 1, 3
- manually checked 1cbs.ccp4 from issue #76 (also a 2, 1, 3)
  and orientation is now correct but there is still an offset error
  that needs to be fixed
- update CHANGELOG (and add @tluchko)

Co-authored-by: tluchko <[email protected]>
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use mrcfile library for MRC/CCP4 file parsing MDAnalysis/GridDataFormats
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@orbeckst @nezix