How to make images for publication using VMD

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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.

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:

"C:\Program Files (x86)\University of Illinois\VMD\\tachyon_WIN32.exe" -mediumshade -trans_max_surfaces 1 tmp.dat -res 4096 2048 -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" to read the data file and convert into a bmp with desirable resolution (-res 4096 2048). This is the trick from which we could make good images. Usually I use 4096x2048 which takes a little bit long time of rendering but provides more than enough resolution you need.

If you have transparent surface, add this option: -trans_max_surfaces [1 to 5], it seems 1 work better. Source refers to here

Detailed options for tachyon render refers to 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.

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