Superimpose two proteins

Question

[iamsmor]

Hi everyone

I tried superimposed two protein with different size

But I get error when I run

line 27, in <module> superimposer.set_atoms(query_atoms, target_atoms) 
line 36, in set_atoms
    raise PDBException("Fixed and moving atom lists differ in size")
Bio.PDB.PDBExceptions.PDBException: Fixed and moving atom lists differ in size

Here I understand my query is 366 and target atoms is 284 length. How can I solve this problem? Thank you

Answer 1

[colindaven]

Do they have the same fold ? Whats' the blast percentage identity between the two ?

I only remember calculating RMS from two superimposed proteins in UCSF Chimera I think (that was ages ago).

But shouldn't you be doing a very important pairwise alignment first ? Think I used MODELLER for this.

[iamsmor]

I also blast this proeints ı get two e-vaue results for aligment length: 676 e value: 0.300109 and length: 676 e value: 3.96561but for A chain for both protein but when ı super imposed ı get size for 6UFO 366 and 4XMB 284 and RMS: 17.92137454675 ı dont understand why size different like this

[colindaven]

You need a percent identity over 35% for them to be the same fold. You didn't state the identity, but it sounds nowhere like this. I don't think these proteins are anywhere near close enough to be aligned and compared.

[iamsmor]

thank you rso much. but ı how ı show idedntity for pertange in my script

Answer 2

[Joe]

I'd advise just using the MatchMaker tool in UCSF Chimera. It's a very matured implementation at this stage, and will handle proteins of different sizes etc.

[iamsmor]

thank you