Hi Enrico,

Your script seems to define a function without actually calling it.  You would need a “delete_unmatched_chains(session)” at the end of the script for it to actually do anything.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Apr 26, 2025, at 1:57 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX Users,

I am trying to perform a morphing between two cryo-EM structures of the same complex, where one structure has twice the number of chains as the other (PDBs 3J9K and 8Y6Q). However, the larger structure causes an error during morphing.

I have attempted to write a script that aligns the two structures and deletes the unmatched chains from the larger structure. Unfortunately, the script is not working as expected.

from chimerax.core.commands import run

def delete_unmatched_chains(session):

# Get models #1 and #2

m1 = next((m for m in session.models if m.id == (1,)), None)

m2 = next((m for m in session.models if m.id == (2,)), None)

if m1 is None or m2 is None:

session.logger.info("Model #1 or #2 not found.")

return

chains1 = {chain.chain_id for chain in m1.chains}

chains2 = {chain.chain_id for chain in m2.chains}

unmatched = chains1 - chains2

if unmatched:

chain_ids = ",".join(unmatched)

# Deleting unmatched chains

run(session, f"delete /{chain_ids}")

session.logger.info(f"Deleted chains: {', '.join(unmatched)}")

else:

session.logger.info("No unmatched chains found.")

Could you please help me or alternatively propose another solution? Any suggestions would be greatly appreciated.

Thank you in advance !

Enrico

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