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 _______________________________________
