Apologies - Slightly off topic request for collaboration from a sculptor, but it does relate to how Pymol works
I am a sculptor working on an ambitious bronze sculpture of DNA and I am looking to find out some more detailed measurements of ideal B-DNA which I am having difficulty getting from Pymol.
You can see my previous work on my website:
The sculpture I am making represents a single turn of ideal B-DNA at a scale of 500 million times life size, i.e. it will be 1m wide by 1.66m tall. Each atom is represented by a small human figure made of bronze, with the bonds between them represented by the arms and legs of the figures.
I studied biochemistry at Oxford in the mid-90s and did a specialisation in DNA dynamics so I am not altogether wet behind the ears, but as I spend most of my time now with plaster and clay, my in depth DNA knowledge is a bit weak and I'm new to Pymol. I have been working from the ideal B-DNA PDB file for all my measurements.
I am at the stage that I have made all 20 bases, and 20 sections of sugar phosphate backbone in bronze, and I am about to start constructing my double helix around a stainless steel central access.
1. I haven't worked out how to get the central axis of B-DNA to appear on Pymol. Is there a way to do this?
If not, I would need a scale drawings of both base pairs with the central axis point (of B-DNA) marked. This would allow me to make various measurements to ensure I put the bases and sugar phospate sections together accurately.
(In particular I need to know the distance between the central axis and the N of each base pair that attaches to the backbone, and the angle between these two lines within each base pair 'rung')
2. I was looking for advice on whether I can safely ignore the base pair axis inclination (as this is only 1.2° I think so) and the propelor twist of the base pairs (I was less sure about this). I think I can straightening up the base pairs but ensure that where they attach to the backbone stays in the same place. I'm hoping the only effect might be on the length and orientation of the hydrogen bonds.
3. Final question for now - is there a standard colour convention for representation of bases like there is for atoms? FYI, I had contemplated doing the patina (colouring) of the sculpture according to the atomic colour code, but with about 1000 atoms, this would be a very fiddly long job. I am now considering colouring each base a different colour and was wondering if there was a standard, such as Adenine is always represented blue, etc..
Many thanks in advance for any help you can give.