Tools For Single Residue Flexible Alignment

Question

[Flow]

I have two PDB protein structures and would just like to do flexible alignment of one residue from structure A to another residue (of the same type) from structure B. I know pymol can do rigid alignment but wonder about tools for this purpose of flexible alignment.

PS: I realized that the Sculpting function in Pymol helps me for my main objective.

Answer 1

[dimkal]

In Maestro (Schrodinger, free for Academic users) you can do superimposition of two proteins based on their structure. After you can 'right click' on the residue of interest, and pick one of several rotamers, and see which aligns the best to your reference structure.

Just curious, why do you need to this?

[Flow]

I would like to check whether a set of 2 residues could potentially align to same residues from another protein for which backbone RMSD is very low

[dimkal]

in that case i think Maestro provides the right amount of interactivity for that... unless you want it automated.