Make images for publication using VMD

原文地址
首先,需要明确的是,VMD能用来生成很漂亮的图片!
先通过此网站对 Tachyon 进行render做初步的了解。

流程:

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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

其中,render这一步包括两个步骤:1) render the current senen to tmp.dat as a data file, 2) use tachyon_WIN32.exe or tachyon_MACOSXX86 to convert tmp.dat to a bmp picture.

render也可以在 Tk console 中完成 render Tachyon tmp.dat exec "C:\\VMD\\tachyon_WIN32.exe" -aasamples 12 tmp.dat -format BMP -o image.bmp

设定输出图像的分辨率 add this option: -res 800 600

设置透明表面 add this option: -trans_max_surfaces [1 to 5], it seems 1 work better. Source refers to here
当然,还需要在representation中设置显示为Surf,并设置Material为 Transparent?

Ambient Occlusion (AO, 环境光遮蔽)
在 Display|Display Settings 中打开(selecting “on” in “Amb. Occl” and “Shadows” ), 调整”AO Ambient” and “AO Direct” 系数(which scale the lighting contribution from the ambient light, and from the standard VMD lights, respectively). 通常情况下,ambient系数在0.7 - 1.0之间,direct 系数在0.1 - 0.4之间,默认值分别为0.8和0.3.

Material in Graphical Representations
Material 的选择最影响最终的显示效果,对于设定了 AO的,建议使用”Diffuse”, or the AO-optimized “AOshiny”, “AOChalky”, or “AOEdgy”.

输出图像格式
以上输出的图像为bmp格式,一般需要再转换为png或jpg等格式。
默认的tachyon不能输出为png格式,但自己手动编译tachyon后放在对应的路径,就可以通过 -format PNG选项来指定输出为png格式的图片。

注意:

  1. transparent surface会降低render的速度(QuickSurf会更慢?)
  2. AO的参数需要自己多尝试,进行调整
  3. AO Ambient 0.8, AO Direct 0.4 is recommended for trans_max_surfaces 1
  4. You might also want to specify your draw material to be AOChalky in order to have the best visual effect under AO.
  5. EdgyGlass is a good choice for material. GlassBubble also gives funny effects
  6. If you think it is too dark, increase AO Direct by 0.1, e.g. 0.8 0.4.
  7. If you think it is a little bit too bright after that, decrease AO Ambient by 0.2, e.g. 0.6 0.4.

其它有用的教程
VMD Images and Movies Tutorial
Detailed options for tachyon here
User’s Guide for tachyon here
VMD View Change Rendering Tutorial