The definitive doer's guide to carma

The examples that follow pertain to the latest version of carma (v.1.0b at the time of writing) and assume that you are using the GNU/Linux executable on a GNU/Linux machine. Furthermore, it will be assumed throughout that you are familiar with things like segment identifiers, atom identifiers, PSF file preparation, etc.

The material is organised in a form suitable for doers: there is no discussion of the keywords or flags, and no discussion of the algorithms, just how to use the program to do something very specific. To use this page: find what you are looking for from the list on the right, click on it, read and do what the relevant section describes.

Just give

carma my.dcd my.psf

and press enter two times. You should see something similar to this (but larger):

While viewing the trajectory, use the keys 'x', 'y', and 'z' to select orthogonal view. Press the 'P' key to pause. Change the zoom with the '<' and '>' keys. Press 'S' to enter stereo (side-by-side) mode. Press the 'ESC' key to swing it (or to stop swinging it). Use the arrow keys to navigate. Press 'R' to reset translations. Press 'P' to exit pause mode (and continue viewing the trajectory). You can change the step (stride) by pressing the '+' and '-' keys. Additionally, for DCD files containing unit cell information, carma can produce a very primitive graphical representation of a volume containing 2x2x2 cells. To do this, press 'B' while viewing the trajectory, and you should see something similar to this:

If your protein comprises, say, two segments with SEGIDs A & B, give

carma -v -w -fit -atmid ALLID -segid A -segid B all_atoms.dcd all_atoms.psf

and then

carma carma.fitted.dcd carma.selected_atoms.psf

You should see a trajectory of the protein atoms only with the rotations & translations removed.

Note well: the carma.selected_atoms.psf file is not a proper PSF file (actually, it is not a PSF file, fullstop). It is only useful for use with carma and can not and should not be used with any other program. You have been warned. The proper PSF file to use in the example shown above would be a protein-only PSF file (as produced, for example, from psfgen).

As a bonus, you will also get a file named carma.fit-rms.dat containing the evolution of the RMS deviation from the starting structure (first frame in the DCD file). Make a plot of it using something like

xmgrace carma.fit-rms.dat

or, if you are an old guy still working on a RedHat 7.3 system you will probably use something like

xmgr carma.fit-rms.dat

If your protein comprises, say, two segments with SEGIDs A & B, give

carma -v -w -fit -atmid ALLID -segid A -segid B all_atoms.dcd all_atoms.psf

and then

carma carma.fitted.dcd carma.selected_atoms.psf

You should see a trajectory of the protein atoms only with the rotations & translations removed.

Note well: the carma.selected_atoms.psf file is not a proper PSF file (actually, it is not a PSF file, fullstop). It is only useful for use with carma and can not and should not be used with any other program. You have been warned. The proper PSF file to use in the example shown above would be a protein-only PSF file (as produced, for example, from psfgen).

You will also get a file named carma.fit-rms.dat containing the evolution of the RMS deviation from the starting structure (first frame in the DCD file). Make a plot of it using something like

xmgrace carma.fit-rms.dat