Re: [PyMOL] Structure alignment -- general question

[Ali Saad Kusay via PyMOL-users]

Hi George,

You can do pairwise alignments, i.e. align 3 of the structures to one structure.

You can also use the "extra_fit" method 
(https://pymolwiki.org/index.php/Extra_fit), i.e:

extra_fit name CA, "object", super

Replace object with the structure you want the other 3 to align to, this uses 
the "super" alignment method but you can also use "align", "cealign", "fit", 
etc. Depending on what gives the best results. Just a note, this will align all 
PyMOL objects to your selected object, you can make sub selections as needed.

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health

On 4/1/22, 8:52 pm, "George Tzotzos via PyMOL-users" 
 wrote:

I’m dealing with 4 heterogeneous structures belonging to the same fold. I’d 
like to compare some conserved structural features and for this purpose it 
would be useful that the structures are aligned and then visualised in a grid.

I understand that the align command works for 2 structures only. Is there 
another way achieve what I described above.

Looking forward to any suggestions

Many thanks in advance and all the best for 2022




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Re: [PyMOL] Structure alignment -- general question

[Saurabh Gayali]

extra_fit command will work in this scenario.

More information in documentation here:
https://pymolwiki.org/index.php/Extra_fit

--

*Saurabh Gayali* / Post Doctoral Fellow
saurabh.gay...@gmail.com / +91 8800412916

*CSIR-IGIB*
New Delhi, India


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04/01/22,
04:18:41 pm

On Tue, Jan 4, 2022 at 3:18 PM George Tzotzos via PyMOL-users <
pymol-users@lists.sourceforge.net> wrote:

> I’m dealing with 4 heterogeneous structures belonging to the same fold.
> I’d like to compare some conserved structural features and for this purpose
> it would be useful that the structures are aligned and then visualised in a
> grid.
>
> I understand that the align command works for 2 structures only. Is there
> another way achieve what I described above.
>
> Looking forward to any suggestions
>
> Many thanks in advance and all the best for 2022
>
>
>
>
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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