#23 read DCD files

[AGrossfield]

It would be very convenient if PyMol could directly read DCD files (the binary coordinate output format for CHARMM and NAMD). This would be useful in 2 contexts: making movies, and observing structure change in a trajectory. In the former case (and perhaps in the latter), one can emulate the ability by reading a series of pdb files, but having a single dcd file is simpler.

If PyMol had this ability, it would allow me to drop VMD once and for all -- this is the only area where VMD is superior.

Alan

[Nobody/Anonymous]

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In the latest release of pymol ( 1.0 and later) you can read dcd files form CHARMM or NAMD (yet I just tried with the first format). To do this, you need to load a pdb file that correspond to your dynamic system, then you can either load the dcd file using the browser if it has the same name as the pdb file or by using command line " load_traj foo.dcd, foo_object" (in this case, foo_object is your pdb).

if you want to go faster, you can type directly in a shell : pymol foo.pdb foo.dcd

Hope it will help

[Warren L. DeLano]

Actually, PyMOL has had this capability for quite some time, through integration of VMD's reader plugins. Generally speaking, however, PyMOL's performance playing MD trajectories isn't competitive with VMD.

However, a new defer_builds_mode=5 was just added to address that shortcoming if you can make do with line and sphere representations (especially sphere_mode=5 if shaders are compiled in).