147 reputation
6
bio website en.wikipedia.org/wiki/…
location Townsville, Australia
age 20
visits member for 2 years, 6 months
seen May 5 at 13:35

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.

Jul
9
comment Is it possible to prove that projectiles with drag will not travel in a parabola under the theory of classical mechanics?
Done, sorry for the mix up.
May
13
comment Is it possible to obtain higher order corrections to the ideal gas law when one allows realistic phenomena to make their way into the equations?
Rofl na it's perfect! Thanks! I didn't know it existed