True, PyMOL doesn't write secondary structure to PDB files, but it does save the current in both PyMOL sessions as well as in PKL (Python Pickle) files.
alter chain A, ss='S'
alter chain B, ss='H'
save example.pkl, 1hpv
From: Paola Beassoni [mailto:paobeassoni@...]
Sent: Tuesday, July 21, 2009 12:27 PM
Subject: [PyMOL] about secondary structure assignement: help
Dear Pymol Users,
i am working with some pdb files with no secondary structures assignments embedded on it. Then when i try to see my molecules on cartoon diagrams, i see the secondary structure different to another programs, VMD for example.
I used the command alter (for example alter 10-34/, ss='S'), and i am capable of assign the secondary structure that i want but this is just temporary. If i save the molecule, when i oppen it again it has the original secondary structure and no the altered one.
Can anyone help me about this??? I really prefer pymol instead other programs for visualization!
Paola Beassoni - PhD
Dpto. Biologia Molecular - FCEFQyN
Universidad Nacional de Rio Cuarto
Río Cuarto - Argentina