142 reputation
6
bio website en.wikipedia.org/wiki/…
location Townsville, Australia
age 20
visits member for 2 years, 6 months
seen May 24 at 4:56

An enthusiast of many trades, mostly science-related. I love to create chemical structure diagrams (both skeletal and 3D), to do so I use:1

  • Accelrys DS Visualizer (ADSV), which I use to make 3D models of small molecules mostly. I usually export them to PNGs with a width of 4,000 px with a background colour that is easy to remove in GIMP. Then in GIMP I remove the background colour using colour to alpha (Colours->Colour to Alpha...) function. I then crop it using autocrop (Image->Autocrop Image).

    ADSV cannot be installed on Ubuntu, or so I believe, so I use it on my Windows 7 machine.

  • MarvinSketch, which I use to make skeletal structures. The structures MarvinSketch creates include some whitespace in the element labels, which I remove in a text editor (e.g., SciTE on Ubuntu) by deleting all mention of xml:space="preserve" using Find & Replace tools. I also remove empty space in the diagram in Inkscape.

    MarvinSketch is free for non-commercial use, although it is not available in the software centre and must be downloaded (from here) and installed (it is provided as a shell script, see here for how to install it).

  • PyMOL, which I use to make 3D models of macromolecules and macromolecule-ligand complexes. I usually render the macromolecule as cartoons, coloured according to secondary structure and the small molecules I depict as ball and sticks or just sticks and colour their atoms according to the element to which they belong (in a style resembling CPK, except with carbons coloured black).

    I use commands like:

    set ray_opaque_background, 0
    png "Pics.png", width = 4000, height = 2325, dpi=800, ray=1
    

    to create a transparent image of the structure at 4,000 px to. The latest vesion of PyMOL can be installed by running the commands here. The software I use to refine these structures, SciTE, Inkscape and GIMP, they can all be downloaded from the software centre or APT. From APT the following should install them all:

    sudo apt-get install gimp inkscape scite
    

Examples of structures I've made may be found on Wikimedia Commons (where I go by Fuse809), here.

Notes

  1. Hyperlinks are to their download site.

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