Abstract chemistry fractal gimp jmol pymol

Source (link to git-repo or to original if based on someone elses unmodified work): Add the source-code for this project on opencode.net


These wallpapers were generated using open-source software only.

# Releases 20180520 and 20180522
They're a Mandelbrot fractal (created using default settings in GIMP) with 3D models, generated in Jmol, of four different chemotherapy drugs on it. I essentially took the models and placed them on a Mandelbrot fractal background in GIMP and exported as a PNG.

The data used to create the 3D models (i.e. where each atom is, the types of bond between atoms, etc.) was taken from X-ray crystallography data, or PubChem entries, or RCSB PDB and optimized using Avogadro2 (https://github.com/OpenChemistry/avogadroapp). The specific chemotherapy drugs were:

* Doxorubicin (top left), created from RCSB PDB DM2 entry (http://www.rcsb.org/ligand/DM2)
* Imatinib (top right), created from RCSB PDB STI entry (http://www.rcsb.org/ligand/STI)
* Cyclophosphamide (bottom left), created from COD 2005356 entry (http://www.crystallography.net/cod/2005356.html)
* Methotrexate (bottom right), created from PubChem CID 126941 (https://pubchem.ncbi.nlm.nih.gov/compound/126941)

They were chosen based on the fact they are arguably the most important members of their respective class of chemo drug (anthracyclines, tyrosine kinase inhibitors, alkylating agents and antimetabolites, respectively). All four are on the World Health Organization's Model List of Essential Medicines (http://www.who.int/medicines/services/essmedicines_def/en/).

# 20180530
This model is based on the PDB entry 3EIG, which is of dihydrofolate reductase (DHFR) in complex with methotrexate. It was created in Jmol. Didn't put a fractal in its background as it would be obscured by the image.

# 20180601
This model is built using PyMOL, GIMP and Inkscape (which I used to treat the legend). It is of 5J2T (http://www.rcsb.org/structure/5J2T), which is of a tubulin-vinblastine complex. Vinblastine is another WHO-EM listed drug, it works by binding to and altering tubulin shape and it is this unique shape of tubulin that is crucial to its use in the assembly of microtubules, which in turn are required for cell division.

# 20180604
This model was also built using PyMOL, GIMP and Inkscape (for the legend). It is of 4TVJ (https://www.rcsb.org/structure/4TVJ), which is a X-ray crystallography experiment performed on recombinant (expressed in E. coli) human Poly ADP-ribose polymerase 2 (PARP2) bound by the fairly recently approved drug, olaparib, and glycerol. By binding to this enzyme olaparib produces antineoplastic effects against cancers bearing genetic defects in single strand DNA break-repairing enzymes like BRCA2.

# 20180607
Also created using PyMOL and GIMP, no need for Inkscape this time. It is of 1PWC (https://www.rcsb.org/structure/1PWC), which is data from a X-ray crystallography experiment performed on DD-transpeptidase from the Streptomyces R61 strain, bound with benzylpenicillin (or penicillin G as its USAN is) after its beta-lactam ring broke open, due to ring strain, and covalently bound itself to serine #62 on the DD-transpeptidase enzyme. It is this covalent binding between benzylpenicillin, after its beta-lactam ring came open, and serine #62 that underpins the therapeutic effect of benzylpenicillin on sensitive gram-positive bacterial infections, as this prevents the DD-transpeptidse enzyme from being able to perform its critical function in helping to maintain the constantly changing cell wall of the bacterium. Without a properly maintained cell wall the bacterium dies.

# 20180630
These include a picture of Catharanthus roseus (Madagascar/Rosy periwinkle), taken from Wikimedia Commons (https://commons.wikimedia.org/wiki/File:Catharanthus_roseus_aka_rosy_periwinkle_7154.JPG), which has its own free license, with a 3D model of the vinblastine molecule.
==Colouring scheme==
The colour scheme for the molecules (not the ribbons) is:
Carbon — black.
Chlorine — green.
Hydrogen — white.
Nitrogen — blue.
Oxygen — red.
Phosphorus — orange.
Last changelog:

20180522 3 years ago

Redid image with cyclophosphamide re-drawn, there was a little bug in the last cyclophosphamide model, the Cl(2) atom had the top of it cut off.

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20180522 3 years ago

Redid image with cyclophosphamide re-drawn, there was a little bug in the last cyclophosphamide model, the Cl(2) atom had the top of it cut off.

Be the first to comment
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