[PyMOL] PDB post-processing and TER records

[James S. <jms...@gm...>]

Dear Pymol Users!

I need to process input PDB via pymol (this time no need to do it via
no-gui mode!!) to remove chain id from PDB.

I am using alter command to do it with the following syntax
#rename chain A to phantom chain :-)
alter (chain A),chain=''

the problem that in my initial PDBs there are many TER records (e.g.
to separate protein from ligand etc), which should be keeped after
such post-processing in the form of original PDB (with chain A).

I have tried to do this before saving of the PDB
get pdb_use_ter_records

however, as the result, all the TER records were removed from the
processed pdb. How I could fix it?

Many thanks in advance!