I think that PyMOL can only align different objects, not different
selections. There may be a more elegant way, but ..
If your chains are A,B,C..H, try this from the PyMOL prompt to create
different objects:
for c in 'A B C D E F G H'.split():cmd.create(c+'_chain','chain '+c)
and this to align them to the first one:
for c in 'A B C D E F G H'.split(): cmd.align(c+'_chain','A_chain')
If you just want a main chain alignment, you can try this:
for c in 'A B C D E F G H'.split(): cmd.align(c+'_chain and name ca','A_chain
and name ca')
etc.
If you're going to do this in a script where you don't know what the
chains are in advance, you try something like this
from pymol import stored,cmd
stored.chains = {}
cmd.iterate('all','stored.chains[chain]=1')
stored.chains = stored.chains.keys()
first = stored.chains[0] + '_chain'
for c in stored.chains():
cmd.create(c+'_chain','chain '+c)
cmd.align(c+'_chain',first)
(that first part is a little slow for large files)
-michael
p.s. I just tried "align A_chain,B_chain,object=thing" for the first
time .. that's pretty cool.
--
This isn't a democracy;| _ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
On Tue, 1 Jun 2004, 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
>
>
>
>
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