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AndrewCRMartin / absplit

Code to split an antibody PDB file into Fv fragments with their antigens
GNU General Public License v3.0
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Summary of problem files #27

Closed AndrewCRMartin closed 1 year ago

AndrewCRMartin commented 1 year ago

The following all have remaining problems:


5kov - problem with H chain - weird chain names
       0P - ok but chain duplicated
       1P - ok but chain duplicated
       2P - not numbered (.bad) - confused by chain labels
       3P - ok but chain duplicated
       4P - ok? perhaps missing partner chain
       5P - OK
       6  - ok? perhaps missing partner chain
       7P - ok but chain duplicated

5wb1 - OK but chain duplicated.
       HC only Ab with Nter fusion. absplit is working but
       numbering is duplicating the Ab 

6e9q 
       0  - heavy chain missing (in SEQRES but not in ATOM)
       1P - heavy chain missing (in SEQRES but not in ATOM)
       2  - heavy chain missing (in SEQRES but not in ATOM)
       3  - heavy chain missing (in SEQRES but not in ATOM)

These all fail in numbering - they are now correctly provided as un-numbered (.bad) files:

1i3u - lost Ab in numbering - fixed to create a .bad file
3mlr - lost Ab in numbering - fixed to create a .bad file
3mls - lost Ab in numbering - fixed to create a .bad file
5dt1 - lost Ab in numbering - fixed to create a .bad file
5w1m - lost Ab in numbering - fixed to create a .bad file
5ywp - lost Ab in numbering - fixed to create a .bad file
6utk - lost Ab in numbering - fixed to create a .bad file
6uuh - lost Ab in numbering - fixed to create a .bad file
6uum - lost Ab in numbering - fixed to create a .bad file
6v6w - lost Ab in numbering - fixed to create a .bad file
6xzf - lost Ab in numbering - fixed to create a .bad file
4b50 - lost all - fixed to create a .bad file
4rqq - lost all - fixed to create a .bad file
4toy - lost all - fixed to create a .bad file
5mp6 - lost all - fixed to create a .bad file
5w1g - lost all - fixed to create a .bad file
5ywf - lost all - fixed to create a .bad file
6y0e - lost all - fixed to create a .bad file
6vtt - lost Ab / lost all - fixed to create a .bad file
7aej - lost Ab / lost all - fixed to create a .bad file
1i3v - lost Ab / lost all - fixed to create a .bad file
3mlt - lost Ab / lost all - fixed to create a .bad file
6qd6 - lost Ab / lost all - 1,2,4,5,7,8 are .bad; 0,3,9 are OK
6y1r - lost Ab / lost all - fixed to create a .bad file
4tvp - fixed for some - fixed to create a .bad file for the bad ones
5fyj - fixed for some - fixed to create a .bad file for the bad ones
5fyk - fixed for some - fixed to create a .bad file for the bad ones
5fyl - fixed for some - fixed to create a .bad file for the bad ones
5u7m - fixed for some - fixed to create a .bad file for the bad ones
5u7o - fixed for some - fixed to create a .bad file for the bad ones
5utf - fixed for some - fixed to create a .bad file for the bad ones
5uty - fixed for some - fixed to create a .bad file for the bad ones
5wdu - fixed for some - fixed to create a .bad file for the bad ones
6ch7 - fixed for some - fixed to create a .bad file for the bad ones
6ch8 - fixed for some - fixed to create a .bad file for the bad ones
6ch9 - fixed for some - fixed to create a .bad file for the bad ones
6de7 - fixed for some - fixed to create a .bad file for the bad ones
6chb - fixed for some / lost all - fixed to create .bad for bad ones
5uy3 - fixed for some / lost all - fixed to create .bad for bad ones
       (The bad one finds one chain as antigen since it doesn't pair them)

The following that were broken are all now fixed:

3wbd
5d9q 
5gru
5ud9 
6qb4 
6qb9 
6qf9
6qfc
6w9g
6xv8 
5nm0
2znx
AndrewCRMartin commented 1 year ago

Believed all to be fixed now (though some cannot be numbered).