Dear,

cealign,super,super_all  cannot make an alignment object , as the most important thing is to obtain
 the alignment file out of all this exercise remains unresolved ,Please suggest me structure based 
alignment method in PyMol wherein I can use multiple structures at a time (with low sequence identity) . 

Pavan Payghan
 
 
 



On Fri, Dec 30, 2011 at 2:15 AM, Thomas Holder <speleo3@users.sourceforge.net> wrote:
PAVAN PAYGHAN wrote, On 12/29/11 13:23:

Dear ,

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

It's different.

The first method uses "align" and gives you an alignment object (uses util.mass_align function).

The second uses "cealign" and cannot make an alignment object.

http://pymolwiki.org/index.php/Align
http://pymolwiki.org/index.php/Cealign

"align" does sequence based alignment and RMSD minimization, "cealign" is a more sophisticated structure based alignment.

Cheers,
 Thomas

Pavan Payghan



On Thu, Dec 29, 2011 at 4:23 PM, zjxu <zjxu@mail.shcnc.ac.cn <mailto:zjxu@mail.shcnc.ac.cn>> wrote:

   Dear Pavan,


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

   check cealign: http://www.pymolwiki.org/index.php/Cealign
   <http://www.pymolwiki.org/index.php/Cealign>

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

   Hope this helps,

   Zhijian Xu


   PAVAN PAYGHAN wrote:


       Dear,

                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
       <speleo3@users.sourceforge.net
       <mailto:speleo3@users.sourceforge.net>
       <mailto:speleo3@users.sourceforge.net

       <mailto:speleo3@users.sourceforge.net>>> 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
                   structures.


          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



          Cheers,
           Thomas

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

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