Is there a way to calculate the backbone RMSD for two different peptides that have the same number of residues but one of the side chains is different? It should be possible because the two peptides will have identical backbones. I have tried the usual interfaces like Superpose and VMD but nothing seems to have this feature. Any ideas?
Dear David,
you might want to save only the backbone coordinates of the peptides in separate files and load those to VMD.
There you can open
Extensions -> Analysis -> RMSD calculator
Select "all" (there are only BB atoms now). Then press Align and then press RMSD.
I hope this is what you mean. I just tried it and it worked for me.
Best regards,
Martin
In coot you can use the Least-squares fitting algorithm to force the alignment of any macromolecular chains. To use this feature, open the two peptide structures in coot, select Calculate> LSQ-Superpose a pop-up box will appear titled Least Squares Fit. Select the reference molecule and the moving molecule in the drop down menu and enter the residue ranges you want to superpose. Select mainchain and select fit. This will force the residues in the listed range to superpose (in the GUI) and calculate an RMSD (displayed in the terminal).
If you have an interrupted chain (say a residue insertion residues 1-20 fit onto residues 1-16) you can open LSQKAB in refmac5 and generate a list of Least-Squares fitting ranges and use this generated file to superpose the mainchains (fit residues 1-10 of molecule A to 1-10 of molecule B AND fit 15-20 of molecule A to 11-16 of molecule B).
Dear David,
In Pymol, if you open both structures as different objects and then align them, the r.m.s.d value, as well as the number of atoms used for the calculus, will appear in your terminal.
Best regards,
Filipa.
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