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)
