set volume_data_range, 0.5 # prune the data range MIN/MAX to be -/+ 0.5 SD
set volume_layers, 1024 # add more layers; slower but cleaner rendering
set volume_layers, 64 # fewer layers, uglier, but faster
do not workusing software renderers, eg. running 32-bit PyMOL on a 64-bit machine, or possibly across the network, and in some VMs.
set ray_volume, 1before ray tracing.
Pre-integrated volume rendering is the new default in Incentive PyMOL 1.7.2. It reduces layering artefacts significantly which are often seen on steep color gradients and/or a low number of volume_layers. It comes at a slightly higher computation cost.
It's now possible to put custom color ramps into a script or your pymolrc to be used as a named coloring preset. Example:
# example data fetch 1ubq, type=2fofc, async=0 # register a new ramp named "blue1yellow2" volume_ramp_new blue1yellow2, \ 1.0 blue 0.3 \ 2.0 yellow 0.2 # use the ramp with the "volume" command volume myvol, 1ubq_2fofc, blue1yellow2
The named color ramp will also show up in the “Action > volume > …” menu of map objects, and in the “Color > …” menu of volume objects.
Adjusting volume colors is easiest done with the interactive volume panel (“Color > panel” in the menu of volume objects). After fine-tuning, you can get the color ramp script with the volume_color command, for re-use like in the example above:
PyMOL>volume_color myvol ### cut below here and paste into script ### cmd.volume_ramp_new('ramp863', [\ 1.00, 0.00, 0.00, 1.00, 0.30, \ 2.00, 1.00, 1.00, 0.00, 0.20, \ 3.31, 1.00, 0.15, 0.98, 0.00, \ ]) ### cut above here and paste into script ###
The script dump will assign a random name (“ramp863” in the example above).