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Build function works three times before being unable to find source anchor atom #438

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kylefisch opened this issue Feb 28, 2025 · 0 comments

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@kylefisch
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kylefisch commented Feb 28, 2025

Describe the bug

The first two build functions to acetylate the n-termini of a polypeptide work fine. The third build function works, but throws an error. The fourth build does not work. By building the first two acetylations, saving the PDB, then opening it again, all chains can be acetylated.

To Reproduce

Steps to reproduce the behavior:

  1. Load the 5O3L PDB
  2. Use one of the two options below three times on different chains:
    PyMOL>editor.attach_amino_acid("chain A and resi 306 and name N", 'ace')
    Where the chain identity changes
    ctrl+middle mouse to select the n-terminal nitrogen, then build >> Residue >> Acetyl
  3. See error:
    Selector-Error: Invalid domain selection name "_tmp_editor_dom".
    Selector-Error: Invalid domain selection name "_tmp_editor_dom".
    Error: Invalid input selection(s)
  4. Perform step 2 one more time:
  5. See error:
    Selector-Error: Invalid domain selection name "_tmp_editor_con".
  6. Perform step 2 one more time:
  7. See error:
    Error: no coordinate for source anchor atom

Expected behavior

Since the first two build functions work, I would expect the same commands/mouse actions would not start failing at some point.

Screenshots

PyMOL>editor.attach_amino_acid("chain A and resi 306 and name N", 'ace')
PyMOL>editor.attach_amino_acid("chain B and resi 306 and name N", 'ace')
PyMOL>editor.attach_amino_acid("chain C and resi 306 and name N", 'ace')
Selector-Error: Invalid domain selection name "_tmp_editor_dom".
Selector-Error: Invalid domain selection name "_tmp_editor_dom".
Error: Invalid input selection(s)
PyMOL>editor.attach_amino_acid("chain D and resi 306 and name N", 'ace')
Selector-Error: Invalid domain selection name "_tmp_editor_con".

PyMOL>editor.attach_amino_acid("chain D and resi 306 and name N", 'ace')
Error: no coordinate for source anchor atom

Environment

Additional context

Add any other context about the problem here.

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