TLDR: This post is a collection of softwares (e.g., VMD and Blender) for visualizing your atomic structures. Personally, I use VMD for quick visualization and Blender for making publication-ready figures.

VMD (ver 1.9.4a51)

I am a user of MacOS, and I prefer working with scripts rather than GUI. Therefore, I will show how to work with tcl scripts in VMD, which make the whole process much easier to be repeated.

General references

Modify your startup files

The default setup of VMD is far from satisfactory for myself. In addition, there are some specify styles I would like to set up for my own work. Therefore, it will be convenient to modify the startup files of VMD, rather than doing it every time I start VMD.

  1. find VMDDIR
    • run puts $::env(VMDDIR) in vmd command line. This would return the path of VMD.
    • (Optional: MacOS) set VMDDIR as env var: export VMDDIR="/Applications/VMD.app/Contents/vmd" in ~/.bash_profile (You should be able to do similar things in Linux.)

  2. link executable files

    # Ubuntu 22.04
export VMDDIR="/home/jxzhu/apps/vmd/1.9.3/lib/vmd"
VMDOS="LINUXAMD64"

# MacOS
# export VMDDIR="/Applications/VMD.app/Contents/vmd"
# VMDOS="MACOSXARM64"

cd $VMDDIR
# soft link remove os suffix
ln -sf stride_$VMDOS stride
ln -sf surf_$VMDOS surf
ln -sf tachyon_$VMDOS tachyon
ln -sf vmd_$VMDOS vmd

  3. modify default setting

    cd $VMDDIR && vi .vmdrc

    # ... append what you want to change

mol default color Element
mol default material Diffuse
mol default style {CPK 1.000000 0.000000 10.0 1.0}

# set default display
display projection Orthographic
display depthcue off

# set background color to white
color Display Background white

# modify RGB for default yellow
color change rgb yellow 1.000000 0.800200 0.200000

# set default color for elements
color Element Pt silver
color Element Au yellow
color Element Na orange3
color Element K violet2
color Element Cs mauve
color Element F cyan3
color Element Cl lime
color Element X gray

References

Work with TCL scripts

It will be nice if I can save all commands for visualization in a script and run it in VMD. This is exactly what TCL scripts are for. Let’s see how it works.

If you can call vmd in the command line, for example, in Linux and MacOS, you can run the following command to start VMD:

# if you don't want to have the GUI, especially for remote connection
# use `-dispdev none`
vmd -dispdev none
source plot.tcl
...

# or
vmd -dispdev none -e plot.tcl
# you can aslo have the GUI with `vmd -e plot.tcl`

If you don’t want to use the command line in your OS, you can also run the TCL script in the VMD console: open tk console (see how to find it) & source tcl file.

In principle, you can also run the commands one by one in the tk console.

References

Track TCL commands

Sometimes, if you are not sure what the corresponding command of a GUI operation is, you can use the logfile command to record all the commands you are using in VMD.

# start logging to vmd.log
logfile vmd.log
# stop logging
logfile off

References

Render

You have gotten a good snapshot! How to save it as a high resolution picture?

If you want to use Tachyon renderer in the TCL script, you need to specify the Tachyon executable in your system. You should be able to find the executable file tachyon_* under $VMDDIR. For convenience, you can make a soft link from the executable to tachyon in the same directory, so that you will not need to modify your scripts when using it on different systems. Then, you can use the following command in the TCL script:

# output is $fname.tga
render Tachyon $fname "$VMDDIR/tachyon" -aasamples 12 %s -format TARGA -o %s.tga -res 1920 1920

In the GUI, you can go to File -> Render, and choose Tachyon as the renderer. The default resolution is not high enough for publication. The default command is:

# the Tachyon executable might be different in your system
"/Applications/VMD.app/Contents/vmd/tachyon_MACOSXARM64" -aasamples 12 %s -format TARGA -o %s.tga

You can specify the resolution by appending -res 1600 1200 to the command. The final command should look like this:

"/Applications/VMD.app/Contents/vmd/tachyon_MACOSXARM64" -aasamples 12 %s -format TARGA -o %s.tga -res 1920 1920

References

Load plugins

Sometimes, you might want to load some plugins, such as pbc, by adding the following command in the beginning of the TCL script:

package require pbctools

You can also find guide in the reference about loading the plugin automatically by modifying the .vmdrc file.

References

Blender (ver 4.4.3)

Compared with VMD, Blender is a more powerful tool for visualization. You can use it to create high-quality figures for publication. While Blender is a free and open-source 3D creation suite for general purposes, it can be used for molecular visualization with the help of the following add-ons:

You can find the first two add-ons in the Blender add-on repository: Edit -> Preferences -> Get Extensions. For the final one, Beautiful Atoms, you need to install it manually. You can find the installation instructions in the documentation.

For MacOS, it is important to put the application in the path where you have write permission (which is not true for Applications normally). And only the manual installation works for me:

# check your path
cd /Applications/Blender.app/Contents/Resources/3.4/python/bin
# change the python executable to the one in your path
./python3.10 -m ensurepip
./python3.10 -m pip install --upgrade pip
# I cannot find pip executable in the path, so I use the following commands
# rather than `./pip install`
./python3.10 -m pip install --upgrade ase
./python3.10 -m pip install --upgrade scikit-image

Then install batoms add-on in Blender as guided in the documentation.

(I still cannot load this add-on in the Blender python console, but I can use it in the Blender GUI. I will update this post if I find a solution.)

Using Blender From The Command Line