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 <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>
>
> 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>>>
>> 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
>>
>>
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