Re: [PyMOL] about secondary structure assignement: help

[Warren D. <wa...@de...>]

Paola,
 
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.
 
load $TUT/1hpv.pdb
 
as cartoon
 
alter chain A, ss='S'

alter chain B, ss='H'
 
rebuild
 
save example.pkl, 1hpv
 
delete all
 
load example.pkl

as cartoon

Cheers,
Warren

 

________________________________

	From: Paola Beassoni [mailto:pao...@gm...] 
	Sent: Tuesday, July 21, 2009 12:27 PM
	To: pym...@li...
	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!
	Thanks!
	
	Paola
	-- 
	Paola Beassoni - PhD
	Dpto. Biologia Molecular - FCEFQyN
	Universidad Nacional de Rio Cuarto
	Río Cuarto - Argentina
	00-54-358-4676422
	00-54-358-4676232 (Fax)