> Please let me know how can I renumber protein chains to avoid overlap and
> give it a uniqu chain id.
>

You can manually modify chain IDs with the alter
<http://pymolwiki.org/index.php/Alter> command. For instance, to rename
chain A to X:

alter chain A, chain = "X"

To automatically select unique chain IDs, you can install the flatten_obj
<http://pymolwiki.org/index.php/Flatten_obj> script.


> How can I change .pse file to .pdb file?
>

Use the 'Save molecule' option in the file menu, or the save
<http://pymolwiki.org/index.php/Save> command.

-Spencer
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