[Biopython] superimposing problem

[George Devaniranjan]

Thanks João for trying.
I was also thinking that you would have to deform the 2nd coil to get
exactly what I want.

What I tried and not completly sussefully but  I will try that agian is as
follows.

1) Superimpose 1st residue of coil1 with 1st residue of coil2, rot/tran
coil2 and get the coordinates---lets call the rot/tran coil2   as mod_coil2

2) Superimpose last residue of coil1 with last residue of mod_coil2 and then
rot/tran whole molecule---the result is not exactly what I want but it is
the only solution I can think of for now.
Thanks once agin João,

George

On Tue, Dec 7, 2010 at 5:40 PM, João Rodrigues <anaryin at gmail.com> wrote:

> 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!
>>>
>>
>>
>