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Areaimol task#125

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stuartjamesmcnicholas wants to merge 12 commits intomainfrom
areaimol
Open

Areaimol task#125
stuartjamesmcnicholas wants to merge 12 commits intomainfrom
areaimol

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@stuartjamesmcnicholas stuartjamesmcnicholas commented Feb 12, 2026

As requested in https://github.com/ccp4/ccp4i2-issues/issues/111 an Areaimol task.

This task offers:

  • basic DIFFMODE OFF functionality to calculate SAS and produce output file with either atom, residue averaged or GXGRATIO "normalised" areas in "B-factor" column.
  • DIFFMODE IMOL to calculate surface of intermoleculat contacts using a symmetry translation in each direction. Output can be by atom or residue averaged.
  • DIFFMODE COMPARE to compare the surface area of 2 models. The residue numbers must be matched in order for this to work. Output can be by atom or residue averaged.
  • EXCLUDE keyword for space separated list of residue types to exclude from calculation.

NB. DIFFMODE WATERS is not supported because it does not appear to work. The WATER example in $CCP4/examples/unix/runnable/areaimol.exam crashes when running from command line.

@stuartjamesmcnicholas stuartjamesmcnicholas marked this pull request as draft February 12, 2026 11:15
@stuartjamesmcnicholas stuartjamesmcnicholas marked this pull request as ready for review February 12, 2026 11:24
@stuartjamesmcnicholas stuartjamesmcnicholas marked this pull request as draft February 13, 2026 09:03
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I have reverted to draft. I have decided the report should be prettier.

@stuartjamesmcnicholas
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I see no easy way to override the font-family of a pre without altering CCP4ReportParser.py or xreport.css. pre is probably the correct way to display the space formatted log file text. So I am minded to leave things as is and declare this ready for review.

@stuartjamesmcnicholas stuartjamesmcnicholas marked this pull request as ready for review February 13, 2026 16:02
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