August 31, 2015
The ChimeraX pdbimages command does batch rendering of molecular assemblies defined in mmCIF files. It makes an image for each assembly in each mmCIF file (*.cif suffix) in a specified directory.
Start ChimeraX and enter the pdbimages command specifying a directory containing mmCIF files:
This will create images for each assembly in the same directory
$ ls /tmp/mmcif_files 1A0M.cif 1EJ6_XAU.png 1M4X_5.png 1A0M_1.png 1GOS.cif 1M4X_6.png 1A2P.cif 1GOS_1.png 1M4X_PAU.png 1A2P_1.png 1IDI.cif 1OJD.cif 1A2P_2.png 1IDI_1.png 1OJD_1.png 1A2P_3.png 1JJ2.cif 1OJD_2.png 1EJ6.cif 1JJ2_1.png 1OJD_3.png 1EJ6_1.png 1M4X.cif 1OJD_4.png 1EJ6_2.png 1M4X_1.png 1OJD_5.png 1EJ6_3.png 1M4X_2.png 1EJ6_4.png 1M4X_3.png 1EJ6_PAU.png 1M4X_4.png
The name of each assembly (typical assembly names are "1", "2", "3"...) is appended to the file mmCIF name to produce the PNG image file name.
A tiled single image showing the assemblies can be made with the free ImageMagick software package using command to make 100 by 100 pixel tile for each assembly image.
montage -label "%t" *.png -geometry "100x100+0+0" tiled.jpg
The assemblies are viewed along the -z axis of the crystallographic coordinates, which is not ideal in many cases. They are shown with atoms as spheres, with separate colors for each chain, and ambient occlusion lighting (which makes recessed areas dark, and allows good depth perception).
The sphere style, coloring, lighting and view point are currently set in the Python code for the pdbimages command. With some knowledge of Python this can be customized. The code is found in the Mac app in
Some of the available commands that could be used to provide different renderings are illustrated in the ChimeraX Quick Start Guide and more details is in the Programming Manual.
There are additional options to the pdbimages command. The command is not yet documented in the User Guide but is listed in the Programming Manual. The following example makes 800 by 800 pixel images, with edge smoothing using supersampling and logs the files processed in the specified file (useful when errors occur).
pdbimages /tmp/mmcif_files width 800 height 800 supersample 3 logFile /tmp/mmcif_files/log
The pdbimages command can be used on a Linux server without graphics and with no display by starting Linux ChimeraX with the --nogui --offscreen flags and then typing the pdbimages command to the resulting ChimeraX prompt. This uses CPU rendering which tests showed to be approximately 60 times slower than rendering with a graphics card and display. It is currently not possible to use a graphics card without a display in ChimeraX.
On a 2012 iMac with 32 Gbytes of memory and Geforce GTX 680MX graphics (2 Gb graphics memory) all assemblies in the PDB can be rendered in about 1 day. Various problems are encountered. The Mac graphics driver typically crashes after about 10,000 mmCIF files. Also ChimeraX uses gradually more memory, even though the mmCIF files are closed after each is rendered. This consumes about 1.5 Mbytes of memory per file, so 10,000 files takes 15 Gbytes of memory. For both these reasons, it is necessary to run in batches of a few thousand files.