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Re: [PyMOL] about super_all.py Plugin installation.
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From: Thomas H. <sp...@us...> - 2011-12-30 09:50:46
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Dear Pavan,
I'm sorry that this appears to be so complicated. The "super" command in
PyMOL is structure based (not as good as cealign) and can create
alignment objects.
The closest solution to your request that I can think of at the moment
is the piece of script below. You can copy-paste this into the PyMOL
command line (including the "python"/"python end" lines).
python
# example structures
cmd.fetch('1e4y 1ake 4ake 3hpq', async=0)
# all to one alignment
target = '1ake' # <-- you can change this
sele = ' and name CA'
models = cmd.get_object_list()
for model in models:
cmd.super(model + sele, target + sele, object='aln')
# save alignment to file
cmd.save('all-to-one.aln', 'aln')
python end
Hope that helps.
Cheers,
Thomas
PAVAN PAYGHAN wrote, On 12/30/11 07:21:
> 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
> <sp...@us... <mailto:sp...@us...>>
> 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/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
>
>
>
> On Thu, Dec 29, 2011 at 4:23 PM, zjxu <zj...@ma...
> <mailto:zj...@ma...> <mailto:zj...@ma...
> <mailto:zj...@ma...>>> 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>
> <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
> <sp...@us...
> <mailto:sp...@us...>
> <mailto:sp...@us...
> <mailto:sp...@us...>>
> <mailto:sp...@us...
> <mailto:sp...@us...>
>
> <mailto:sp...@us...
> <mailto:sp...@us...>>>> 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
>
>
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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