No it doesn't, both in Fedora 11 and Ubuntu 9.04. I get:
NameError: global name 'cealign' is not defined
Thomas
> Thomas,
>
> The command
>
> cmd.do(".../cealign.py")
>
> runs cealign.py, which runs cmd.extend. So you should have the cealign
> command in your namespace after the cmd.do. Have you
Thomas,
The command
cmd.do(".../cealign.py")
runs cealign.py, which runs cmd.extend. So you should have the cealign
command in your namespace after the cmd.do. Have you tried running
cmd.do("your/path/to/cealign")
cealign(protA, protB)?
I just tried this on my system and it worked for me. Let
> Thomas,
>
> The PyMOL UI runs asynchronously. I think you are deleting your PDB
> files before they can be aligned. I made a couple changes in your
> script. Instead of calling cmd.do just call cealign directly. See
> below,
>
> query_template_chains = {
> "1ebh" : ["1ebg", "1els", "1one", "2on
> Message: 6
> Date: Thu, 29 Oct 2009 13:40:56 +0200
> From: Thomas Evangelidis
> Subject: Re: [PyMOL] how to get RMSD from CEalign command
> To: Andreas Forster
> Cc: pymol-users@lists.sourceforge.net
> Message-ID: <20091029134056.136077awqo817...@webmail.duth.gr>
Thank you Adnreas.
I'm straggling with cealign now. When I run it in batch mode I get
"Selector-Error: Invalid selection name" for certain structures, which
in fact are very close homologs, whereas the number of RMSD values I
get varies (sometimes 3, 5, etc). Here's the code:
query_template
