Aligning in PyMol
PDB ID 1h9t contains a structure of both a DNA and a protein. It starts as one object.
Before we perform an alignment, we need to separate your DNA from the protein.
Show sequence (click the S at the bottom right).
Highlight all the "residues" from the chains X and Y (these chains contain each strand of your DNA) in the sequence ...
This article will probably be informative for you:
Looking at Structures: Introduction to Biological Assemblies and the PDB Archive
The PDB file contains the asymmetric unit found in a particular crystallographic study. The biological assembly is the quaternary structure known or predicted to be found in living systems. For many proteins (but not 2PJY), the ...
You can use "as" to switch to a particular style (http://pymolwiki.org/index.php/As
as cartooon, 11AS and chain a
You can also hide everything, to remove all representations (http://pymolwiki.org/index.php/Hide):
hide every, 11AS and not (n. ca+c+n and resi 5-10)
I'm a fairly expert user of PyMOL and I've never seen an API exposed which will show ...
It seems that if no HELIX record is present in the PDB, PyMol attempts to assign secondary structure itself. For whatever reason, it does not do this if multiple MODELs are present. You should be able to use the dss command to force PyMol to calculate secondary structure in a PDB with multiple MODELs.