[Biopython] superimposing problem

[George Devaniranjan]

Oh now I see what you mean--ok what I did was actually convert all residues
EXCEPT (if present that is) GLY and PRO to ALA
So all residues in both structures I think end up being the same in the
given example so then I tried what I suggested. I will try again tomorrow
what Peter suggested.
Thank you once again to you both for the help.
George

On Tue, Dec 7, 2010 at 11:33 PM, João Rodrigues <anaryin at gmail.com> wrote:

> The problem here is that for that picture to be possible you have to have
> exactly similar flanking residues. And in those structure of yours, it seems
> you don't.
>
> Peter was trying to find a way of making sure that the superimposition was
> unambiguous. In other words, that the loops superimposed in the only way
> possible (rotation- and translation-wise). By having more than one point per
> residue, as you are doing with those CA, C, N and O atoms, you're getting
> the best superimposition possible. However, since the ends of the loop do
> not match, you can never fit them as in the picture.
>
> I'm assuming you're generating these loops out of loop modelling program of
> sampling program. Try adding dummy residues before and after the loops, say
> two ALAs, and fix them during the procedure. If, on the other hand, you want
> a good measure of displaying loop flexibility/variability, try superimposing
> only the first residue. That should be unique enough to display the
> different conformations.
>
> Sorry I can't be of much help...
>
>
> João [...] Rodrigues
> http://doeidoei.wordpress.com
>
>
>
> On Wed, Dec 8, 2010 at 12:18 AM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hello Peter,
>> Thank you for your suggestion.
>> I am using CA/C/N/O  for superimposition of S1/S2 and E1/E2.
>>
>> Not sure I got exactly what you meant but I am going to think about it
>> tonight  and see if that makes sense.
>>
>> The idea that I am trying to see is ---if 2 coils from diff protein have
>> approximately the same length (S1-E1  = S2-E2 distance) and have the same
>> number of residues what is the "floppiness" or (no of conformations) that
>> you can see.
>>
>> So as in my figure I sent (reattached) it does not matter where the
>> intermediate residues are they can flop about.
>> Thanks I will think about this more in the next few days.
>> Regards,
>> George
>>
>>
>>
>>
>> On Tue, Dec 7, 2010 at 6:00 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:
>>
>>> On Tue, Dec 7, 2010 at 10:49 PM, George Devaniranjan
>>> <devaniranjan at gmail.com> wrote:
>>> > 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
>>>
>>> Hi George,
>>>
>>> Hopefully I have understood your aim, and the following makes
>>> sense...
>>>
>>> Have you thought about (in your head - no code needed) trying to
>>> simultaneously try to superimpose the first residues AND the last
>>> residues with a rigid body motion (rotation and translation)?
>>>
>>> Assuming you are using just the C-alpha atoms for this. Lets
>>> call these atoms S1, E1 and S2, E2 (start and end). Also
>>> suppose that the distance S1 to E1 is bigger than S2 to E2.
>>> The superposition will  give you S1, S2, E2, E1 on a line in space.
>>> However, the relative rotation of the two loops is free.
>>>
>>> So, if using C-alpha atoms,  I think you are going to have to include
>>> at least one pair of atoms from the loop, e.g. M1 and M2 for the
>>> C-alpha of the mid point residue.
>>>
>>> However, if you are using more than just the C-alpha atoms, that
>>> should give enough constraints for the superposition to be unique.
>>> It may still not be what you want, in which case try adding more
>>> constraints as above.
>>>
>>> Peter
>>>
>>
>>
>