Superimpose two proteins
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6 days ago
iamsmor • 0

Hi everyone ı tried superimposed two protein with different size

here my script for superimposing

But get error when ı 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 ı understand my query is 366 and target atoms is 284 length how ı can solve this problem ? thank you

python pymol proteins carbonatom superimpose • 241 views
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6 days ago
colindaven ★ 3.9k

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.

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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

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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.

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

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6 days ago
Joe 20k

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.

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thank you

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