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
http://pymolwiki.org/index.php/TMalign
And also look at these messages at the pymol-users:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/
[PyMOL] Transformation Matrices
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09981.html
[PyMOL] alignment by residue
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09960.html
[PyMOL] how to get the translation vector used in align command
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09553.html
[PyMOL] Multiple Structure Superposition
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09464.html
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.
Jacob,
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.
Cheers,
-- Jason
See here:
http://www.pymolwiki.org/index.php/Linux_Install#Mint_12_compile_and_install_with_MPEG_support
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2012/1/13 QT <rdirect...@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.
>
> Best,
> Quyen
>
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