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To retain the order of the atoms in your PDB file, type this “magic command”:

set retain_order,1

Note: this is OK for small molecules but can give rise to serious problems if the object is a protein or a peptide, particularly if site-point mutagenesis is performed (in this case, set retain_order,0)

Other commands that can be helpful sometimes are:

set pdb_retain_ids,1

set pdb_no_end_record,1

To save a session for a previous version of PyMOL, e.g. 1.6:

set pse_export_version, 1.6
save 16compat.pse

To save a publication-quality image file:

png fileName, dpi=600

To monitor phi/psi angles in object/selection:

phi_psi obj/sele

magic_commands.txt · Last modified: 2019/09/18 12:18 (external edit)