On Dec 7, 2023, at 7:16 PM, Ellen Shrock via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

for res in list(chimera.selection.residues):

This should be:

from chimera.selection import currentResidues

for res in currententResidues():

There is no easy way to get the findclash command to append to a file.  You would have to open the file yourself, call the underlying findclash Python function, parse the results and format it into the output file.  Probably easier to just concatenate the files afterward with the Unix 'cat' command.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab