Module to RMSD two proteins with Python?
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5.5 years ago
becko • 0

I have two protein structures in PDB format. The two structures refer to two conformations of the same protein. I want to calculate the RMSD between them.

Is there Python module that will allow me to do this?

python protein-structure • 8.0k views
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Hello j.cossio.diaz!

It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/34534589

This is typically not recommended as it runs the risk of annoying people in both communities.

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You can try pymol or tm align
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You can try pymol or tm align
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5.5 years ago

Hi j.cossio.diaz

I struggled with the same problem and i find two module which can solve structural protein alignment in python.

You can explore the algorithm by using examples, which are exist in the zip file. The only think you have to do is extract the "ATOMS" with x,y,z coordinates from PDB files.

2. There is also a tool call biopython, which have a Bio.PDB module to align PDB files. here is the link: http://combichem.blogspot.com.tr/2013/08/aligning-pdb-structures-with-biopython.html

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4.3 years ago
crooveck ▴ 10

You can use PyMOL to calculate alignment. To do this follow this steps:

1. run PyMOL
2. type this command to load your proteins: fetch pdbId1 and fetch pdbId2 *
3. Use command: rms_cur pdbId1, pdbId2 to calculate RMSD value betweend your structures

--

*where pdbId1 and pdbId2 is identifier of your protein in PDB database.

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4.3 years ago
Joe 19k

A UCSF Chimera option:

(Taken from a more complicated script I wrote for use with pychimera here: script, pychimera)

NB, pychimera takes a little more involved installation compared to pymol, but I really like it.

The code below should work inside chimera's python interpreter though I believe with no extra configuration.

from MatchMaker import (match,
CP_BEST,
GAP_OPEN,
GAP_EXTEND,
defaults,
MATRIX,
ITER_CUTOFF)

chimera.openModels.open(model1,type="PDB")
chimera.openModels.open(model2,type="PDB")

all_models = chimera.openModels.list(modelTypes=[chimera.Molecule])
mod0 = all_models[0]
mod1 = all_models[1]

for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST,[mod0, mod1],defaults[MATRIX],
"nw",defaults[GAP_OPEN],defaults[GAP_EXTEND]):

mol0_name = atoms2[0].molecule
mol1_name = atoms1[0].molecule
printmol0_name.name + "\t" + mol2_name.name + "\t" + str(rmsd))

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4.3 years ago
Eric T. ★ 2.7k

In Biopython, the Bio.SVDSuperimposer class will quickly align the two PDB structures and compute the RMSD. See this Bio.PDB FAQ, and search the page for "RMSD", or read the PDB section of the Biopython tutorial.

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Hi, I know this might be very late to comment to it, but Bio.SVDSuperimposer does not seem to rotate the proteins to get the lowest RMSD: i get RMSD = 0.2 for chains that when aligned in PyMOL give RMSD = 0.06

here is my code:

fixed = Bio.PDB.Selection.unfold_entities(Bio.PDB.Polypeptide.PPBuilder().build_peptides(Bio.PDB.PDBParser(QUIET = True).get_structure('X' , '1A00_B.pdb') , aa_only = True)[0], 'A')
moving = Bio.PDB.Selection.unfold_entities(Bio.PDB.Polypeptide.PPBuilder().build_peptides(Bio.PDB.PDBParser(QUIET = True).get_structure('X' , '1A00_D.pdb') , aa_only = True)[0], 'A')

sup = Bio.PDB.Superimposer()
sup.set_atoms(fixed , moving)
print(sup.rms)
sup.apply(moving)
print(sup.rms)

OUTPUT:
0.199679715722
0.199679715722


the "sup.apply(moving)" line does not seem to do anything.

Is this the correct way to find the RMSD between two structures in Biopython? is there a better script to write? or a better module to use than Biopython?