Inside a script, I would suggest adding ",async=0" so that the fetch command
is forced to complete before the next command is read:

fetch 1a25, async=0
show cartoon
create chaina, chain a
...
...

--
Subject: Re: [PyMOL] pdb-l: chain alignment tool

Hi,

There are many. One way is to use PyMol (or, indeed many other viewers). So
I did it like this:

fetch 1a25
show cartoon
create chaina, chain a
create chainb, chain b
delete 1a25
align chaina, chainb
color red, chain a
color blue, chain b

I guess that this could be generalised into a script to align the chains of
any dimer.

gilleain

On Mon, Jul 7, 2008 at 3:51 PM, David Hoksza <hok...@ksi.ms.mff.cuni.cz>
wrote:
> Hi, don't anybody of you know if there exists a tool, that can 
> visually align two protein chains? I.e. 1a25a and 1a25b seem very 
> similar to me and I would like to visually confirm or disprove this 
> fact.
>
> Thank you,
>      David
>


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