[Biopython] superimposing problem

[João Rodrigues]

Hello George,

I've tried restricting the alignment to a few atoms only. It works perfectly
for one residue only, but when you add a second residue it probably tries to
fit both (which it pretty much impossible unless both starting residues have
exactly the same rotamer) and it doesn't produce exactly what you want.

I'm attaching a pymol session picture of the result of
this<http://pastebin.com/hjk9m6mM>script that superimposes CA, CB, and
HA (more or less a straight line) atoms
of the first residue of both loops. Both loops have a completely different
structure, starting already with a twist on the first ALA residue, so I
think it's pretty hard to do what you want (exactly) without deforming your
loops.

Usually, to produce those figures, you should have anchor residues whose
coordinates remain the same and then generate the loop residues.

I hope someone else can prove me wrong :)

Best,

João [...] Rodrigues
http://doeidoei.wordpress.com



On Tue, Dec 7, 2010 at 10:39 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> sorry message got sent before I finished.
>
> I can do this (connected.jpg)
>
> I want to do this (superimpose.jpg)
>
>
> Thanks
> George
>
> On Tue, Dec 7, 2010 at 4:14 PM, João Rodrigues <anaryin at gmail.com> wrote:
>
>> Hello George,
>>
>> From what I understood, what you want to be compare the diversity of two
>> loops based on anchor points.
>>
>> Peter already pointed you to a great resource here<http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/python/protein_superposition/>
>> .
>>
>> To make it clearer, you should first define the residues you want to align
>> (or the particular atoms) and then perform the alignment.
>>
>> For example, I wanted to align a loop in my protein so I defined the *
>> resi_range* variable to restrict the alignment to those residues.
>> Furthermore, I then made sure that I only used CA atoms with two for loops.
>>
>> Check the code here (http://pastebin.com/V2UsGYGL), might help you
>> understand how it works.
>>
>> Best!
>>
>
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: loop.png
Type: image/png
Size: 11694 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biopython/attachments/20101207/b91ddb6a/attachment-0001.png>