Thanks a lot for the information. As you mentioned super is only for aligning two structures while with super_all to align the multiple structures, but the most important thing is to obtain the alignment file out of all this excercise, can it be possible with super, super_all?

If not which option exist in Pymol wherein one can align 4-5 structures at a time (with low sequence identity).


Pavan Payghan

On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder <> wrote:
Hi Pavan,

Thank you very much for the modified script.

Its working fine, only thing I am facing is that it can not be used for aligning more than two structures at a time(I want it for around 4 -5 structure  alignment). The command used to do so is

super abc,def,XYZ

"super" is for two structures, "super_all" (from the script) is for many structures. But the syntax is without comma in mobile selection:

super_all abc, def ghi jkl

for the third structure its giving error like ,ValueError: invalid literal for float (): XYZ.

Apart form this could you please explain

  1. Number of alignment residues should match exactly in all the

you can't influence this with super_all.

  2. How to get alignment file for super, super_all command after
     alignment has been done.

this is not possible with super_all.

But PyMOL can do this even without the super_all script. On the button-panel to the right, try: "A > align > all to this"

You'll get an new object called like "aln_all_to_XYZ", this you can save:

save file.aln, aln_all_to_XYZ


Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen