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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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6e9q - heavy chains in SEQRES but ATOM records missing #30

Closed AndrewCRMartin closed 1 year ago

AndrewCRMartin commented 1 year ago

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)
AndrewCRMartin commented 1 year ago

Note 1P (Chain C/D) should not be finding chain A (part of 0) as an antigen.

AndrewCRMartin commented 1 year ago

Missing chain is a numbering error (huge CDR-H3 in a bovine antibody).

Now creates a .bad file

AndrewCRMartin commented 1 year ago

Reduced cutoff for antigens to 0.94:

Chain A <=> Domain 3 (chain C)
DOM: VQLRESGPSLVKPSQTLSLTCTASGSDKAVGWVRQAPGKALEWLGSIDTGGNAGYNPGLKSRLSITQDNSKSQVSLSVSTVTTEDSATYYCTTV------NCPAGYSVHYDC---SFGVRHTTYE---DAWGQGLLVTVSS--------------------------------------------------------------------------------------------------------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPSVTLFPPSTEELNTLVCLISDFYPGSVTDGSTIVETTRASKQSNSKYAASSYLTSSDWKSCEVTHEGSTVTKT
CHN: VQLRESGPSLVKPSQTLSLTCTASLSDKAVGWVRQAPGKALEWLGSIDTGGNAGYNPGLKSRLSITQDNS--QVSLSVSTVTTEDSATYYCTTVHQKTTRNCPAGYSVHYDCGRASSISVTYTYEWYVDAWGQGLLVTVSSASTTAPKVYPLSSCCTVTLGCLVSSYMPEPVTVTWNSGALKSGVHTFPAVLQSSGLYSLSSMVTVPGFTCNVAHPASSTKVDKAVEPKSCSSTKVDKAVEPKSC
SCO: 0.944882
AndrewCRMartin commented 1 year ago

All issues now fixed - though a bit of a kludge!