Obtaining the covariance matrix from the MD run has been discussed in detail (see Variance-covariance and cross-correlation analysis). The difficult part is obtaining the covariance matrix from the ensemble of NMR stuctures. The important thing to notice is that by its definition the covariance matrix

*carma*in the usual way to prepare the matrix. Converting a series of PDB files to a DCD file can easily be done with VMD (select molecule, then 'Save coordinates' and chose DCD). The resulting DCD file (from VMD) must be filtered through

*catdcd*

```
catdcd -o mynew.dcd previous.dcd
```

Then run *carma* as before and thats it. You can now compare the two matrices (the example shown below is for native Rop) :

The peaky appearance of the NMR-derived map (on the left) is possibly due to the small number of structures (10 in this case) that were used for the calculation1.