Andreas Foerster <andr...@biochem.utah.edu>: > - The dss algorithm is great, a very quick way to assign secondary > structure. Is there a way of conserving the information when saving the > pdb? There are at least 3 ways to store SS assignments from PyMOL. Depends on your needs:
1. Save PyMOL session (*.pse). Atom properties, including "ss", will be restorable by PyMOL. 2. Print SS in "PHD-like" format. So, assuming that unfamous 1tii.pdb is loaded PyMOL>import pymol PyMOL>stored.ss = [] PyMOL>iterate 1tii//a//ca, stored.ss.append(string.ljust(ss,1)) PyMOL>print string.join(stored.ss,"") will print single string like LSSSSSSLLLHHHHHHHLLLLLLLLLLLLLLLLLLLLLHHHHHHLLLLLLLLLLLSSSSSLLHHHHHHHHHHHHLLLLSSSSSSSSLLL LSSSHHHHHLLLLLLHHHLLSSSSLLLLHHHLSSSSSSSLLLLLLLLLLLLLLLHHHHLLLLLLLHHHHHHHLLLLLLLHHHHLLHHHH HLLHHHLL 3. Wait for Warren to vivify cSetting_save_pdb_ss :) > Sometimes it's nice to edit the assignment. I haven't understood your question. You might edit dss assignment just by PyMOL>alter pk1, ss='S' Is it sufficient? -igor
