Hi Briony,
this sounds like a very cool project!
Regarding question 1: If your PDB DNA model is long enough, you can use
cafit_orientation from the psico module (a PyMOL extension) to draw
the axis. It determines the axis by least-square linear fit on the
backbone atoms. This requires a recent PyMOL version and numpy.
If the helix is not long enough, cafit_orientation will most likely
result in a slightly skewed axis, but I think you need a perfect axis,
right? If you are interested, I could customize the script to take the
bases orientations into account when interpolating the axis. Just let me
know.
http://www.pymolwiki.org/index.php/psico
Cheers,
Thomas
Briony Marshall (Personal) wrote, On 01/07/13 17:43:
Apologies - Slightly off topic request for collaboration from a
sculptor, but it does relate to how Pymol works
Dear all,
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:
http://www.briony.com
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.
(this is a much more complicated version of this sculpture I did
previously based on the structure of
diamond: http://www.briony.com/works/dream-II_1.html)
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.
Regards
Briony
Briony Marshall - Sculptor
www.briony.com http://www.briony.com/
http://www.briony.com/join my mailing
list: www.briony.com/subscribe.html http://www.briony.com/subscribe.html
or like me on facebook: www.facebook.com/brionymarshallsculptor
http://www.facebook.com/brionymarshallsculptor
UK mobile: +44 (0)7956 107 893
Pangolin London Sculptor in Residence
blog:
www.a-n.co.uk/link/creative-year http://www.a-n.co.uk/link/creative-year
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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