Tony Giannetti wrote:
Hey everyone,
I know I should be past this, but I can't seem to figure out how to do
this. I have a couple of crystal structures that contain multiple copies in
the asymmetric unit, and I would like to superimpose each copy to see what
the differences are. One way is to break the PDB file into one file for
each chain, but I'm wondering if there's a better way to handle this in
PyMol? One file (1CX8) has 8 copies and the other (1DE4) had three. I
tried split_states but it didn't work. I also tried aligning say chain A
onto chain B directly but that failed too (as expected). Is there a
straightforward way to do this or do I begin splitting these 700 residues
proteins up by hand. I wouldn't ask except it's a recurring problem with
many of the structures we study so I'm wondering if a general solution or
script exists or can be made to deal with this.
Tony
Hi Tony -
I'm sure there's a more elegant way to do this, but since the
coordinates for each chain are in the PDB file sequentially, I usually
just open the file with nedit and copy&paste the blocks of coordinates
into separate files (including the CRYST1 card at the top of each file
and 'END' at the bottom).
Alternately, load the whole thing into Pymol then use 'create':
load 1CX8.pdb, cx8
create cx8_a, cx8 and chain a
create cx8_b, cx8 and chain b
etc.
The new objects can then be aligned.
- Matt
--
Matthew Franklin Phone:(650)225-4596
Postdoctoral Researcher Fax:(650)225-3734
Genentech, Inc.
1 DNA Way, South San Francisco, CA 94080
