Dear All

Many thanks for taking interest in my questions.

I am trying to do a PCA analysis of my md simulated structures that are homodimers. I am using gromacs 'covar' command to do it.

I am having 2 issues:

1. there is a warning that is generated for some structures

WARNING: there are fewer frames in your trajectory than there are degrees of freedom in your system. Only generating the first 1000 out of 3546 eigenvectors and eigenvalues.

2. I am getting a view of only one dimer Calpha chain but not the other although when İ select the chains in pymol, I can see the other chain as dots. I have added my pdb file. As a result, I get errors in the porcupine plot when I want to generate using the python script in pymol.

Any idea why I am getting it? and how to resolve them.

Thank you

Ayesha