[PyMOL] about secondary structure assignement: help

[Paola Beassoni]

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

[Nathaniel Echols]

Post by Paola Beassoni
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!

The most compatible solution is probably to generate the HELIX and SHEET
records for your PDB file, which PyMOL will read (not sure about
VMD). There is an open-source program called KSDSSP that will do this:

http://www.cgl.ucsf.edu/Overview/software.html#ksdssp

I haven't used it very much, but it's supposedly a re-implementation of the
original DSSP algorithm, so theoretically very robust. If you're
continually generating new PDB files (e.g. refining the structure, etc.)
you'll probably need to keep these records in a separate file and paste them
into every new PDB file, since most programs won't retain that information
when writing files. If you don't like the results, it's fairly simple to
modify the records to suit your taste.

Alternately, you can save a PyMOL script containing the alter commands and
just invoke that every time you load your structure.

-Nat

[Warren DeLano]

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:***@gmail.com]
Sent: Tuesday, July 21, 2009 12:27 PM
To: pymol-***@lists.sourceforge.net
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)