Re: [PyMOL] nice DNA pdb and ring options

[Andrew C. <aco...@gm...>]

Hello

You can look into 3DNA out of Rutgers
(http://rutchem.rutgers.edu/~xiangjun/3DNA/).  To make the image you
describe you will also need to use Raster3D.  3DNA has some basic
scripts for this but you will need to write your own to get the image
you describe.

Andrew



On Mon, Feb 23, 2009 at 11:29 AM, H. Adam Steinberg <ad...@st...> wrote:
> I have three questions I'm hoping someone can help with.
>
> 1. Does anyone have, or can anyone point me to a program that will
> generate a nice pdb file that contains 50 or so base pairs of random
> sequence B form DNA with hydrogen bonds between the bases or no H bonds?
>
> I need to be able to scultp the DNA and have one strand react to the
> pulling of the other strand. I also want to show the union of the AT and
> GC via H bonds. The H bonds can be regular bonds (and probably will have
> to be if I'm going to be sculpting). I can make the h bonds and make
> them real bonds for the sculpting, I'm just wondering of anyone has
> already done it or has a script around....
>
> 2. When showing a cartoon of DNA the ribose ring in the backbone is
> always there no matter which setting you choose. How can I make the
> phosphates and the ribose rings show as a backbone cartoon "tube" and
> keep just the bases as filled sticks with rinngs?
>
> 3. Rings on DNA and RNA can be filled, in cartoon mode. But I can't get
> the rings to fill in on selected amino acids (H, W, Y, F) in a protein
> of that same file. Is there a fill amino acid ring setting?
>
> Thanks in advance for anything you can offer,
>
> Adam
>
> --
> _______________________________________
>
> H. Adam Steinberg
> Artist, Scientist
> <http://adam.steinbergs.us>
>
> Information Technology and Media Center
> Department of Biochemistry
> University of Wisconsin-Madison
> 433 Babcock Drive
> Madison, WI 53706
> 608/265-4982
> _______________________________________
>
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