On Tue, Jul 21, 2009 at 12:23 PM, Paola Beassoni <paobeassoni@gmail.com> wrote:
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