Question: RMSD of two homologues proteins
0
gravatar for Mike
5.3 years ago by
Mike0
Warsaw
Mike0 wrote:

Hi,

I'm looking for the easiest way of calculating RMSD between two homologues proteins. (i.e. sequences do not match perfectly). Until now I was using Chimera software, where steps are as follow:

1. Calculating pairwise alignment

2. Then structures are superimposed

3. RMSD is calculated between corresponding amino acids in alignment.

And this work quite well, but I'm looking for something simpler that I can use in python script. Preferably in with no need of running subprocess.

superposition rmsd python • 2.2k views
ADD COMMENTlink modified 5.3 years ago by a.polo88110 • written 5.3 years ago by Mike0
0
gravatar for a.polo88
5.3 years ago by
a.polo88110
Italy
a.polo88110 wrote:

you can create a script for pymol that function with python script or directly from the software can be possible. otherwise there are many of packages in R for example BIO3D can be useful.

https://pypi.python.org/pypi/pyRMSD/4.0.0 can be useful.

 

ADD COMMENTlink written 5.3 years ago by a.polo88110
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