147 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.

Jul
15
asked Where can some worked problems in classical mechanics (and more specifically the Lagrangian and Hamiltonian formalisms) be found?
Jul
9
revised Is it possible to prove that projectiles with drag will not travel in a parabola under the theory of classical mechanics?
Formatting the equation with MathJaX. Plus Earth is a proper noun, hence should be capitalised.
Jul
9
suggested approved edit on Is it possible to prove that projectiles with drag will not travel in a parabola under the theory of classical mechanics?
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.
Jul
9
revised Is it possible to prove that projectiles with drag will not travel in a parabola under the theory of classical mechanics?
deleted 27 characters in body; edited tags; edited title
Jul
9
revised Is it possible to prove that projectiles with drag will not travel in a parabola under the theory of classical mechanics?
added 26 characters in body; edited tags
Jul
9
asked Is it possible to prove that projectiles with drag will not travel in a parabola under the theory of classical mechanics?
Jul
9
awarded  Excavator
Jul
9
revised What exactly are Hamiltonian Mechanics (and Lagrangian mechanics)
Fixing the spelling of University; also decided to link the titles of these textbooks.
Jul
9
suggested approved edit on What exactly are Hamiltonian Mechanics (and Lagrangian mechanics)
Jul
9
revised What exactly are Hamiltonian Mechanics (and Lagrangian mechanics)
Adding links to Amazon for the books mentioned. Also fixing the name of the boas books it's Mathematical Methods of the Physical Sciences, not of Physics.
Jul
9
suggested approved edit on What exactly are Hamiltonian Mechanics (and Lagrangian mechanics)
Jun
13
accepted In Orbital Mechanics what is the quantity described below called?
Jun
13
asked In Orbital Mechanics what is the quantity described below called?
May
13
awarded  Student
May
13
accepted 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?
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
May
13
asked 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?
Jan
27
awarded  Scholar
Jan
27
awarded  Supporter