MBG wiki | RecentChanges | Blog | 2021-10-25 | 2021-10-24

Quick view of large trajectory (DCD) files

Difference (from prior major revision)

Changed: 1c1,9

< <b>/Carma/ is evolving quickly these days. For all examples that follow please add a '-trace' flag to tell /carma/ to draw a backbone trace. There are more new features in /carma/, like stereo viewing, swinging the molecule around, etc. Have a look in /carma/'s manual page.</b>;

to

> <b>/Carma/ is evolving really fast these days. The rest of this page is history (and as such, is being kept). As of v.0.8 of /carma/, you can view a trajectory file quickly by saying :
> <code>
> carma my.dcd my.psf
> </code>
> That's all. Just hit enter to start from the beginning, or select starting frame.
> You should see something like
> [[image: carma version 0.8]]
> -----
> /Carma/ is evolving quickly these days. For all examples that follow please add a '-trace' flag to tell /carma/ to draw a backbone trace. There are more new features in /carma/, like stereo viewing, swinging the molecule around, etc. Have a look in /carma/'s manual page.


Carma is evolving really fast these days. The rest of this page is history (and as such, is being kept). As of v.0.8 of carma, you can view a trajectory file quickly by saying :

carma my.dcd my.psf

That's all. Just hit enter to start from the beginning, or select starting frame.

You should see something like

 carma version 0.8


Carma is evolving quickly these days. For all examples that follow please add a '-trace' flag to tell carma to draw a backbone trace. There are more new features in carma, like stereo viewing, swinging the molecule around, etc. Have a look in carma's manual page.


The most powerful program for viewing trajectory files is vmd. The problem is that vmd attempts to load the whole trajectory file in memory. With the limited physical memory resources available on our nodes (256 MBytes for newer nodes) if you try to run vmd with a dcd larger than 512 MBytes the following will happen :

A quick way to view large DCD files without large memory consumption has been implemented in carma. But : the viewer is primitive, extremely primitive. You can only view things along the three orthogonal axes (x, y, and z), the only representation available is simple dots, and the choice of colours is obscure. Typical. Still, this is how is goes (use the xyz keys to change views):

carma -v -gl 70.0 -atmid "ALLID" protein_only.dcd protein_only.psf

 carma viewer image A

carma -v -gl 70.0 -atmid "ALLID" -segid " A   " -segid " B   " protein_only.dcd protein_only.psf

 carma viewer image B

carma -v -gl 70.0 -segid " A   " -segid " B   " protein_only.dcd protein_only.psf

 carma viewer image B2

carma -v -gl 120.0 -atmid "ALLID" -segid " A   " -segid " B   " protein_only.dcd protein_only.psf

 carma viewer image C

carma -v -gl 90.0 -atmid "ALLID" -segid " A   " -segid " B   " -segid " WT1 " -segid " C   " -segid " D   " -segid " SOD " all_atoms.dcd all_atoms.psf

 carma viewer image D

carma -v -gl 90.0 -atmid " SOD " -atmid " CLA " -atmid " OH2 " all_atoms.dcd all_atoms.psf

 carma viewer image E

carma -v -gl 90.0 -atmid "ALLID" all_atoms.dcd all_atoms.psf

 carma viewer image F