pdb_selaltloc removes insertions in antibodies

[amjjbonvin]

Describe the bug

In the case of e.g. antibodies with insertions in the CDR loops numbered with additional A, B, C..., running pdb_selaltloc will delete the insertions. Those are basically interpreted as alternate locations.

To Reproduce
Steps to reproduce the behavior. Preferrably, a code snippet.

pdb_fetch 1uz8 | pdb_tidy -strict  | pdb_selchain -A | pdb_delhetatm | pdb_selaltloc | pdb_fixinsert | pdb_keepcoord | pdb_tidy -strict |grep " CA " |head -40 >results1.pdb
pdb_fetch 1uz8 | pdb_tidy -strict  | pdb_selchain -A | pdb_delhetatm | pdb_fixinsert | pdb_selaltloc | pdb_keepcoord | pdb_tidy -strict |grep " CA " |head -40 >results2.pdb
diff results1.pdb results2.pdb

Expected behavior

pdb_selaltloc should not delete insertions!

Desktop (please complete the following information):

• OS: Mac OS
• Python Version 3.12.8

[amjjbonvin]

Probably linked in some way to issue #153
Would be good to do something about it as there are now several issues with this tool.