Closed AndrewCRMartin closed 1 year ago
Many of these are now handled fine.
The majority of the rest seem to be cases where the numbering fails.
The following still fail in numbering:
pdb1i3v_0.faa pdb3q6f_0.faa pdb4toy_0.faa pdb5kov_3.faa pdb5wb1_0.faa pdb6qb4_0.faa pdb6v6w_2PH.faa
pdb1i3v_1.faa pdb3q6f_1.faa pdb5d9q_2.faa pdb5kov_4P.faa pdb5wdu_1.faa pdb6qb9_0.faa pdb6v6w_3H.faa
pdb2znx_1.faa pdb3q6f_2.faa pdb5d9q_3PH.faa pdb5kov_5.faa pdb5wdu_2P.faa pdb6qb9_1.faa pdb6w5a_0.faa
pdb2znx_2PH.faa pdb3q6f_3.faa pdb5d9q_4PH.faa pdb5kov_6P.faa pdb5wdu_3.faa pdb6qd6_0.faa pdb6xv8_0.faa
pdb2znx_3.faa pdb3q6f_4.faa pdb5d9q_5.faa pdb5kov_7.faa pdb5wdu_4P.faa pdb6qd6_1.faa pdb6xv8_1.faa
pdb3mlt_2.faa pdb3q6f_5.faa pdb5d9q_6PH.faa pdb5kov_8P.faa pdb5wdu_5.faa pdb6qd6_2.faa pdb6y0e_0.faa
pdb3mlt_3.faa pdb3wbd_1.faa pdb5d9q_7PH.faa pdb5kov_9P.faa pdb5wdu_6PH.faa pdb6qf9_0.faa pdb6y0e_1.faa
pdb3mug_0.faa pdb3wbd_2H.faa pdb5d9q_8.faa pdb5mp6_0.faa pdb5wdu_7PH.faa pdb6qf9_1.faa pdb6y1r_0.faa
pdb3mug_1.faa pdb3wbd_3.faa pdb5dt1_0.faa pdb5mp6_1P.faa pdb5wdu_8PH.faa pdb6qfc_0.faa pdb6y1r_1.faa
pdb3mug_2H.faa pdb4b50_0.faa pdb5gru_3.faa pdb5ud9_0.faa pdb5wdu_9PH.faa pdb6uuh_0.faa pdb6y1r_2.faa
pdb3mug_3.faa pdb4rqq_0.faa pdb5kov_10.faa pdb5uy3_0.faa pdb5ywf_0.faa pdb6uuh_1.faa pdb6y1r_3.faa
pdb3mug_4.faa pdb4rqq_1.faa pdb5kov_1.faa pdb5uy3_1.faa pdb5ywf_1.faa pdb6uum_1.faa pdb6y1r_4.faa
pdb3mug_5H.faa pdb4rqq_2.faa pdb5kov_2P.faa pdb5w1g_0.faa pdb6bjz_0.faa pdb6v6w_1H.faa
Some of these fail in abnum:
pdb1i3v_0.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb1i3v_1.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb3mlt_2.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb3mlt_3.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb4b50_0.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb5mp6_0.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb5mp6_1P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb5w1g_0.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) LFR1_End
pdb6qd6_0.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6qd6_1.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6qd6_2.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6xv8_0.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6xv8_1.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6y0e_0.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_Start
pdb6y0e_1.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_Start
pdb6y1r_0.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6y1r_1.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6y1r_2.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6y1r_3.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb6y1r_4.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb1i3u_0H.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End
pdb3mlr_0P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb3mls_0P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb3mls_1P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb3mls_2P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb3mls_3P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb3mlt_0P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb3mlt_1P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
pdb5nm0_2.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_End HFR3_End
pdb5w1m_0P.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) LFR1_End
pdb5w1m_1P.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) LFR1_End
pdb5w1m_2P.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) LFR1_End
pdb5w1m_3P.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) LFR1_End
pdb6xzf_0P.faa
# Error: Unable to number sequence #1: failed assignment of segment(s) HFR2_Start
pdb7aej_0P.faa
# Error: Unable to number sequence #1: region lengths are out of bounds.
The rest are fails in pdbabnum
rather than abnum
itself.
pdb2znx_1.faa pdb2znx_2PH.faa pdb2znx_3.faa pdb3mug_0.faa pdb3mug_1.faa
pdb3mug_2H.faa pdb3mug_3.faa pdb3mug_4.faa pdb3mug_5H.faa pdb3q6f_0.faa
pdb3q6f_1.faa pdb3q6f_2.faa pdb3q6f_3.faa pdb3q6f_4.faa pdb3q6f_5.faa
pdb3wbd_1.faa pdb3wbd_2H.faa pdb3wbd_3.faa pdb4rqq_0.faa pdb4rqq_1.faa
pdb4rqq_2.faa pdb4toy_0.faa pdb5d9q_2.faa pdb5d9q_3PH.faa pdb5d9q_4PH.faa
pdb5d9q_5.faa pdb5d9q_6PH.faa pdb5d9q_7PH.faa pdb5d9q_8.faa pdb5dt1_0.faa
pdb5gru_3.faa pdb5kov_10.faa pdb5kov_1.faa pdb5kov_2P.faa pdb5kov_3.faa
pdb5kov_4P.faa pdb5kov_5.faa pdb5kov_6P.faa pdb5kov_7.faa pdb5kov_8P.faa
pdb5kov_9P.faa pdb5ud9_0.faa pdb5uy3_0.faa pdb5uy3_1.faa pdb5wb1_0.faa
pdb5wdu_1.faa pdb5wdu_2P.faa pdb5wdu_3.faa pdb5wdu_4P.faa pdb5wdu_5.faa
pdb5wdu_6PH.faa pdb5wdu_7PH.faa pdb5wdu_8PH.faa pdb5wdu_9PH.faa pdb5ywf_0.faa
pdb5ywf_1.faa pdb6bjz_0.faa pdb6qb4_0.faa pdb6qb9_0.faa pdb6qb9_1.faa
pdb6qf9_0.faa pdb6qf9_1.faa pdb6qfc_0.faa pdb6uuh_0.faa pdb6uuh_1.faa
pdb6uum_1.faa pdb6v6w_1H.faa pdb6v6w_2PH.faa pdb6v6w_3H.faa pdb6w5a_0.faa
Some of those that fail are because pdbabnum
doesn't deal with single chains properly - e.g. 6qfc_0
Now OK:
pdb1ahw_0P.faa pdb1s78_0P.faa pdb3lrh_0P.faa pdb3wbd_0H.faa pdb5vm4_3.faa pdb5vm4_7.faa pdb7kqy_2.faa
pdb1ahw_1P.faa pdb1s78_1P.faa pdb3lrh_1P.faa pdb5vm4_0.faa pdb5vm4_4.faa pdb5vm4_8.faa
pdb1p7k_0H.faa pdb1xct_0P.faa pdb3lrh_2P.faa pdb5vm4_1.faa pdb5vm4_5.faa pdb7kqy_0.faa
pdb1p7k_1H.faa pdb1xct_1P.faa pdb3lrh_3P.faa pdb5vm4_2.faa pdb5vm4_6.faa pdb7kqy_1.faa
Now bad PDB codes that need fixing:
1i3u 1i3v 2znx 3mlr 3mls 3mlt 3mug 3q6f 3wbd 4b50
4rqq 4toy 4tvp 5d9q 5dt1 5fyj 5fyk 5fyl 5gru 5kov
5mp6 5nm0 5u7m 5u7o 5ud9 5utf 5uty 5uy3 5w1g 5w1m
5wb1 5wdu 5ywf 5ywp 6bjz 6ch7 6ch8 6ch9 6chb 6de7
6e9q 6qb4 6qb9 6qd6 6qf9 6qfc 6utk 6uuh 6uum 6v6w
6vtt 6w5a 6w9g 6xv8 6xzf 6y0e 6y1r 7aej
Of these, the following are from pdbabnum
fails:
2znx 3mug 3q6f 3wbd 4rqq 4toy 5d9q 5dt1 5gru 5kov
5ud9 5uy3 5wb1 5wdu 5ywf 6bjz 6qb4 6qb9 6qf9 6qfc
6uuh 6uum 6v6w 6w5a
The following are from abnum
fails:
1i3u 1i3v 3mlr 3mls 3mlt 4b50 5mp6 5nm0 5w1g 5w1m
6qd6 6xv8 6xzf 6y0e 6y1r 7aej
The following fail for unidentified reasons:
4tvp 5fyj 5fyk 5fyl 5u7m 5u7o 5utf 5uty 5ywp 6ch7
6ch8 6ch9 6chb 6de7 6e9q 6utk 6vtt 6w9g
Of the pdbabnum
fails:
2znx 3mug 3q6f 3wbd 4rqq 4toy 5d9q 5dt1 5gru 5kov
5ud9 5uy3 5wb1 5wdu 5ywf 6bjz 6qb4 6qb9 6qf9 6qfc
6uuh 6uum 6v6w 6w5a
Non-standard AAs are now working in dbc3d14972e199040dff646e385bcf46bb781222 for
Current fail list:
1i3u - abnum
1i3v - abnum
2znx - scFv - splitting now works, but problem with numbering owing to pdb2pir breaking! - the alignment doesn't work properly
3mlr - region lengths are out of bounds
3mls
3mlt
3wbd - FIXED (Start of patch sequence not found within the first 50 residues of the PDB file)
4b50
4rqq - abnum
4toy - abnum
4tvp - abnum
5d9q - Unable to read patch file **and** Start of patch sequence not found within the first 50 residues of the PDB file
5dt1 - abnum
5fyj
5fyk
5fyl
5gru - Not fixed Start of patch sequence not found within the first 50 residues of the PDB file
5kov - Some abnum fails
5mp6
5nm0
5u7m
5u7o
5ud9 - abnum
5utf
5uty
5uy3 - Patch file: Error: Unable to number sequence 2: region lengths are out of bounds.
5w1g
5w1m
5wb1 - FIXED (Start of patch sequence not found within the first 50 residues of the PDB file) but this is a special case
5wdu - abnum
5ywf - pdbpatchnumbering: Unable to read patch file
5ywp
6ch7
6ch8
6ch9
6chb
6de7
6e9q
6qb4 - FIXED (Start of patch sequence not found within the first 50 residues of the PDB file)
6qb9 - FIXED (Start of patch sequence not found within the first 50 residues of the PDB file)
6qd6
6qf9 - FIXED (Start of patch sequence not found within the first 50 residues of the PDB file)
6qfc - FIXED (Start of patch sequence not found within the first 50 residues of the PDB file)
6utk
6uuh - abnum
6uum - abnum
6v6w - abnum
6vtt
6w9g
6xv8
6xzf
6y0e
6y1r
7aej
Closing this and adding a new summary
Empty:
Missing:
Present but no H/L chains: