How to make a matrix of RMSDs for multiple superimposed proteins?

[Andrew Orry]

Q. How to make a matrix of RMSDs for multiple superimposed proteins?

A. 

The function below will return RMSD matrix between two sets of molecules

 Srmsd(<as_Nmol>,<as_Kmol>,matrix) => M_NxK_superposition_srmsds

E.g:

Srmsd( a_*.A a_*.A matrix  )  # pairwise distances for Nof( a_*.A )

to place Matrix into a table:

myMatrix = Table(Srmsd( a_*.A a_*.A matrix  ))

[Andrew Orry]

Continuing from the last question -  you can add  the object name to the RMSD matrix table as shown below:

You can convert matrix to a table and assign column names from objects names like below:

t = Table( Srmsd( a_*.A a_*.A matrix ) Name( Obj(a_*.A)) )    # assumes single A chain in each object

Row labels cannot be reassigned but you can add column with names

add column t Name( Obj(a_*.A)) name="obj" index=1