Hi QT.

Some of the align functions need to have the same chain name of the residues.
I don't know if that is the issue with super.

Have a look at Thomas Holders new pymol plugin

And also look at these messages at the pymol-users: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/
[PyMOL] Transformation Matrices
[PyMOL] alignment by residue
[PyMOL] how to get the translation vector used in align command
[PyMOL] Multiple Structure Superposition

And then, you may want to have the open source version of pymol, since there have been some corrections lately
to some of the alignment functions.
Thomas Holder apprised me of a detail that effected the cealign code
(I used transform_selection instead of transform_object). This code
has been updated in the open-source repository; matrix_copy should now
work after aligning with cealign.


-- Jason
See here: http://www.pymolwiki.org/index.php/Linux_Install#Mint_12_compile_and_install_with_MPEG_support

Troels Emtekær Linnet
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2012/1/13 QT <rdirective@gmail.com>
Dear all,

I'm having a tough time using the super command correctly.  I want to superimpose two 5S structures.

In pymol, I'll do the following

load 2awb.pdb
load 3cc2.pdb

create ec-5s, 2awb and chain a
create hm-5s, 3cc2 and chain 9

If I issue super ec-5s, hm-5s then the cryptic error "ExecutiveAlign: invalid selections for alignment. would appear."

Issuing super /ec-5s//a, /hm-5s//9 does not help either.

What am I missing?  align /ec-5s//a, /hm-5s//9 works just fine though...

Any help from the community would be very appreciated.

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