Molecular Graphics in VMD

CHAP writes a triangle mesh representation of the computed pore surface to a Wavefront OBJ file. Unfortunately, VMD does not natively support the import of Wavefront OBJ meshes, which is why CHAP comes bundled with Tcl code that supports reading and visualising OBJ files using VMD’s draw command. CHAP also provides a turnkey Tcl script for visualising the permeation pathway together with the channel protein.

Loading and Displaying OBJ Files

The code for loading and displaying OBJ data can by found in the file wobj.tcl, which is located under chap/scripts/visualisation/VMD/ in your CHAP install directory. Assuming that you copied wobj.tcl to your working directory, you can load it into VMD by opening the Tk Console (under Extensions > Tk Console in the VMD menu) and typing:

source wobj.tcl

This will make the functions import_wobj and draw_wobj available. The first of these can be used to load data from an OBJ file and the second function can be used to draw either the entire mesh or individual groups of faces. Both functions are contained within a namespace called WOBJ, so to load data from output.obj, you need to type:

set obj [WOBJ::import_wobj "output.obj"]

You can now display the permeation pathway coloured by e.g. solvent density by typing:

WOBJ::draw_wobj $obj "avg_density"

Note that if the second argument to draw_wobj is a string that does not match any of the group names in output.obj the pore will be drawn in solid colour.

As VMD’s draw command adds elements to the molecule as a whole, it is unfortunately not possible to add different surface colours as individual representations that can be switched off or on through the GUI and pathway visualisation has to be controlled manually through VMD’s Tk console.

Turnkey Visualisation Script

To allow quick visualisation of CHAP results in VMD, the directory chap/scripts/visualisation/VMD/ also contains the Tcl script visualise_pathway.tcl, which loads data from both output.pdb and output.obj to visualise the channel protein together with permeation pathway. Internally, this script uses functions defined in wobj.tcl, so you need to make sure that wobj.tcl is located either in your working directory or in the same directory as visualise_pathway.tcl.

The visualise_pathway.tcl script can be started either from within VMD by typing

source visualise_pathway.tcl

in the Tk console or directly from the command line as part of the VMD invocation by typing:

vmd -e visualise_pathway.tcl

If the second approach is used, wobj.tcl needs to be in the current working directory.

By default, visualise_pathway.tcl assumes that the data files are called output.obj and output.pdb. In order to use custom file names, you need to set the variables FILE_PORE_SURFACE and FILE_STRUCTURE before calling source visualise_pathway.tcl. Similarly, if you want the pathway surface coloured by a specific property, you need to set the variable PROPERTY accordingly. For example, if your data files are named abcd.pdb and pathway.obj and you want the pathway surfaced coloured by solvent density, you need to type the following:

set FILE_STRUCTURE "abcd.pdb"
set FILE_PORE_SURFACE "pathway.obj"
set PROPERTY "avg_density"
source visualise_pathway.tcl

You can also pass arguments to visualise_pathway.tcl if you are loading it at VMD start-up, by using the -args flag to set the PDB file name, OBJ file name, and property name (in this order):

vmd -e visualise_pathway.tcl -args abcd.pdb pathway.obj avg_density

Note that in this case all three arguments need to be set explicitly.