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).
Hi Pavan,"super" is for two structures, "super_all" (from the script) is for many structures. But the syntax is without comma in mobile selection:
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_all abc, def ghi jkl
for the third structure its giving error like ,ValueError: invalid literal for float (): XYZ.1. Number of alignment residues should match exactly in all the
Apart form this could you please explain
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
MPI for Developmental Biology