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 ------------------------------------------------------------------------------ Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
