I'm sorry that this appears to be so complicated. The "super" command in
alignment objects.
is the piece of script below. You can copy-paste this into the PyMOL
command line (including the "python"/"python end" lines).
Hope that helps.
Post by PAVAN PAYGHANDear,
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
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/Align>
http://pymolwiki.org/index.php/Cealign
<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
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>
<http://www.pymolwiki.org/index.php/Cealign
<http://www.pymolwiki.org/index.php/Cealign>>
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
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
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
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
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