align first protein with second protein. You will get RMSD

This could be for your basic studies

code: align protein1, protein2

enter

As suggested in the previous answers, the RMSD of Atomic coordinates between two molecules can be calculated by simply using align or super (It does structure based dynamic programming alignment) commands in the PyMol. Both of these commands when run with default parameters give least values of RMSD but by rejecting the outliers as indicated by Chetanath Neupane

align object1*, object2*, cycles=0, transform=0

*Simply change the names object1 and object2 with your molecules of interest.

Steps to Follow:

1. Open your molecules in PyMol for which you want to calculate the RMSD.

2. Type the command I wrote above in the command line.

3. Press Enter

4. You will get the calculated RMSD in the external window just above the command line.

Regards

Hi

I found pair_fit comment much more useful. It gives the RMSD for all the atoms that you asked for.

e.g. pair_fit b1///2-4/N+CA+C, obj01///5-7/N+CA+C, cycles=0

The attached draft document details the different commands you can use for a least-squares superposition and rmsd determination in PyMOL. As @Chetanath Neupane cited from one of my earlier answers to a similar question, the rmsd values you get depends

Sorry -lost connection.

The attached draft document details the different commands you can use for a least-squares superposition and rmsd determination in PyMOL. As @Chetanath Neupanecited from one of my earlier answers to a similar question, the rmsd values you get depends on exactly how the atoms in the two structures are paired

Have you tried TM-Align?

If you want to calculate the RMSD of whole protein or even the parts, I will suggest you take a look of this vedio:https://www.youtube.com/watch?v=5xXwlD75fRs

1. Generally, fetch protein1(with PDB ID) and protein2 (or you can open your own PDB files)

2. using super (Superimpose is recommended by Pymol: super is more robust than align for proteins with low sequence similarity. ) rather than align:

super protein1, proteins

you can get outputs like this:

MatchAlign: aligning residues (487 vs 494)...  MatchAlign: score 2132.796  ExecutiveAlign: 7352 atoms aligned.  ExecutiveRMS: 515 atoms rejected during cycle 1 (RMSD=1.33).  ExecutiveRMS: 509 atoms rejected during cycle 2 (RMSD=0.84).  ExecutiveRMS: 327 atoms rejected during cycle 3 (RMSD=0.62).  ExecutiveRMS: 182 atoms rejected during cycle 4 (RMSD=0.54).  ExecutiveRMS: 77 atoms rejected during cycle 5 (RMSD=0.51).  Executive: RMSD =    0.494 (5742 to 5742 atoms)

3. If you want to measure the part of the protein, you can select the parts which you want and rename it, then do like above:

super protein1_selection, protein2_selection

More details: https://pymolwiki.org/index.php/Super

I hope this can help,

Good luck!

@Abu Turab Naqvi, thanks for the tutorial in using pymol for calculating rmsd.

Thanks a lot from the bottom of my heart, it did help me a great deal@He Dongchang

Hi,

when I am trying the solution of Abu Turab Naqvi, I don't get any RMSD, Pymol just reads it. What is the problem? My command is

align Spinorbit, singlet, cycles=0, transform=0.

Also, do I need to align those 2 structures before it?

Thank you in advance,

Piotr Szkudlarek

Hello. This value of RMSD calculate in Pymol, what is their unit?

Thanks

Hi, @Ariana Egoavil sorry for the late response.

The most commonly used unit for the RMSD value is Ångström (Å).

https://www.youtube.com/watch?v=p9F3oQF5x9A

https://www.youtube.com/watch?v=i1FuJRj5q8I

GOOD LUCK

You calculate RMSD by finding the square root of the mean square error.

https://www.youtube.com/watch?v=p9F3oQF5x9A

Ariana Egoavil The commonly used unit for RMSD is Angstrom (Å), but you can use 0.1 nanometre, or 100 picometres instead of Å based on your need.