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 <
spel...@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/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 <z...@mail.shcnc.ac.cn <mailto:
>> z...@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>
>>
>> <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
>> <spel...@users.sourceforge.net
>> <mailto:speleo3@users.**sourceforge.net<spel...@users.sourceforge.net>
>> >
>> <mailto:speleo3@users.**sourceforge.net<spel...@users.sourceforge.net>
>>
>>
>> <mailto:speleo3@users.**sourceforge.net<spel...@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
>
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