The carma cookbook

For the examples that follow I will assume that you work on a GNU/linux box, that your favorite x-y graphing program is xmgr and that your postscript viewer is ghostscript.


Getting rid of waters, ions, ..., and removing overall rotations-translations

carma -v -w -fit -atmid ALLID -segid A my.dcd my.psf 1)
xmgr carma.fit-rms.dat 2)
mv carma.fitted.dcd protein.dcd 3)
mv carma.selected_atoms.psf protein.psf 4)


Preparing a Cα-only DCD + PSF, removing overall rotations-translations

carma -v -w -fit protein.dcd protein.psf 5)
mv carma.selected_atoms.psf CAs.psf 6)
mv carma.fitted.dcd CAs.dcd7)
xmgr carma.fit-rms.dat 8)


Dihedral PCA using only φ, ψ angles : First approach

carma -v -w -3d -col -segid A -dPCA 7 3 320 protein.dcd protein.psf 9)
gs carma.dPCA.*.ps 10)
vmd carma.3d_landscape.cns 11)
xmgr carma.dPCA.eigenvalues.dat 12)
xmgr carma.rmsd_vs_clusters.dat 13)

Dihedral PCA using only φ, ψ angles : Structural analysis of first cluster

carma -v -w -3d -col -segid A -dPCA 7 3 320 protein.dcd protein.psf
awk '{if ($2==1) print $1}' carma.clusters.dat > cluster_1.dat
carma -v -sort cluster_1.dat protein.dcd protein.psf
carma -v -fit -atmid ALLID carma.reordered.dcd protein.psf
mv carma.fitted.dcd cluster_1.dcd
mkdir tmp
cd tmp
carma -v -pdb -atmid HEAVY -step 500 ../cluster_1.dcd ../protein.psf
cat *.pdb > ../cluster_1.pdb
cd ..
rm -rf tmp/


Dihedral PCA using φ, ψ and χ1 angles : First approach

carma -v -w -3d -col -segid A -chi1 -dPCA 7 3 320 protein.dcd protein.psf 14)
gs carma.dPCA.*.ps 15)
vmd carma.3d_landscape.cns 16)
xmgr carma.dPCA.eigenvalues.dat 17)
xmgr carma.rmsd_vs_clusters.dat 18)


1) “A” is assumed to be the SEGment IDentifier of the macromolecular component
2) The graph will show the evolution of the RMS deviation vs. frame number from the starting structure using all protein atoms
3) This is the new DCD file containing protein-only atoms with rotations-translations removed
4) , 6) This PSF file is only good for use with carma. It will not work with any other programs that read PSF files
5) Carma's default is to use only the CA atoms, so no -atmid card is needed
7) This is the new DCD file containing only CA atoms with rotations-translations removed
8) The graph will show the evolution of the RMS deviation vs. frame number from the starting structure using only CA atoms
9) 320 is the temperature in K. 7 is the number of principal components that will be calculated. 3 is the number of PCs for all combinations of which 2D distribution plots will be generated
10) The PC distributions
11) The 3D principal component landscape. You'll have to change the RMSD cutoff to see the map
12) The distribution of eigenvalues
13) Number of clusters as a function of RMSD cutoff (for carma)
14) 320 is the temperature in K. 7 is the number of principal components that will be calculated. 3 is the number of PCs for all combinations of which 2D distribution plots will be generated
15) The PC distributions
16) The 3D principal component landscape. You'll have to change the RMSD cutoff to see the map
17) The distribution of eigenvalues
18) Number of clusters as a function of RMSD cutoff (for carma)