Re: [PyMOL] about super_all.py Plugin installation.

[PAVAN P. <pav...@gm...>]

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...> 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
>