How to make images for publication using VMD
Probably the most obvious reason that we use VMD is that it could make very nice images for publication or visual appreciation(?). Creating images with high resolution is of the most importance.
Contents
[hide]Publication Figure Rendering With Tachyon
<Click me!> Please first read this single-slide webpage <Click me!>
I am also attending the journey of learning to render good images. So currently I could only provide you some useful links and my way of rendering. Please feel free to come to discuss with me or edit this page if you have a better way out. --Kevin (talk) 19:41, 14 May 2014 (HKT)
A general and highly recommended mini-tutorial on VMD images and videos is provided here as a web-book. Also I found a very clarifying message with replies from one of the authors of the mini-tutorial in the VMD Mailing List.
Following is my step of rendering:
- Load VMD state of the Molecule.
- Go to File -> Render -> Tachyon
- Use "tmp.dat" for Filename in the render window
- Modify Render Command in the render window as follows:
Windows: "C:\Program Files (x86)\University of Illinois\VMD\\tachyon_WIN32.exe" tmp.dat -format BMP -o path/to/your/image.bmp
Mac: "/Applications/VMD 1.9.1.app/Contents/vmd/tachyon_MACOSXX86" -aasamples 12 tmp.dat -format BMP -o path/to/your/image.bmp
- Start Rendering
You should able to understand what has been done by VMD from the steps. Generally the VMD first renders the current scene to "test.dat" as a data file, then it uses the implemented program - "tachyon_WIN32.exe" or "tachyon_MACOSXX86" to read the data file and convert into a bmp. This is the trick from which we could make good images. Usually I use 2048x1024 which takes a little bit long time of rendering but provides more than enough resolution you need.
Transparent surface
If you have transparent surface, add this option: -trans_max_surfaces [1 to 5], it seems 1 work better. Source refers to here
Resolution
You may manually set the resolution with a desirable one by adding option: -res XXXX XXXX (e.g. -res 2048 1024).
Ambient Occlusion (AO)
Ambient occlusion lighting is enabled in the Display|Display Settings window by selecting "on" in "Amb. Occl" and "Shadows" choosers. Once ambient occlusion lighting is enabled, the effect is adjusted by manipulating the "AO Ambient" and "AO Direct" coefficients, which scale the lighting contribution from the ambient light, and from the standard VMD lights, respectively. In most cases, an ambient light coefficient ranging from 0.7 to 1.0 and a direct lighting coefficient of 0.1 to 0.4 are most appropriate and yield the best results. A rule of thumb that tends to work well is that the sum of the two lighting coefficients should be near to 1.0.
Material in Graphical Representations
It turns that that the material chosen affect the final visual effect most. As AO effect is highly recommended, a material that is fairly diffuse such as "Diffuse", or the AO-optimized "AOshiny", "AOChalky", or "AOEdgy" materials should be used.
Detailed options for tachyon here
But BMP is in fact not a convenient format communicating with LaTex or MediaWiki so we have to further convert it into PNG or JPG or GIF using external graphical software. It remains much to explore. PhotoShop is expected to involve in the future.
