Dear ,

"A > align > all to this"  and  "alignto" both are the same or  different?
If different in what context.

Pavan Payghan

On Thu, Dec 29, 2011 at 4:23 PM, zjxu <> wrote:
Dear Pavan,

align 4-5 structures at a time (with low sequence identity).

check cealign:

In pymol1.4, you could use 'alignto':
PyMOL>help alignto
NOTE: This feature is experimental and unsuspported.
"alignto" aligns all other loaded objects to the given selected object
using the CEalign algorithm.
alignto target [, quiet ]
# fetch some calmodulins
fetch 1cll 1sra 1ggz 1k95, async=0
alignto 1cll

Hope this helps,

Zhijian Xu



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

   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


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