VMD-L Mailing List

From: Pattanayek, Sabuj (sabuj.pattanayek_at_Vanderbilt.Edu)
Date: Mon Jun 14 2004 - 13:30:18 CDT

Hi,

In the pdb http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1GQU (1GQU) the base
plane on the terminal adenines are not being filled in with a color in
ribbons/new ribbons representation mode. This is the full "residue" entry for
one of these adenines from the pdb.

ATOM 1 O5* A A 1 14.601 32.388 17.726 1.00 17.14 O
ATOM 2 C5* A A 1 13.677 32.341 16.637 1.00 18.40 C
ATOM 3 C4* A A 1 12.606 31.306 16.895 1.00 18.40 C
ATOM 4 O4* A A 1 13.178 29.974 16.821 1.00 18.40 O
ATOM 5 C3* A A 1 11.974 31.399 18.281 1.00 18.40 C
ATOM 6 O3* A A 1 10.584 31.064 18.177 1.00 18.40 O
ATOM 7 C2* A A 1 12.755 30.371 19.082 1.00 18.40 C
ATOM 8 C1* A A 1 12.977 29.295 18.044 1.00 18.40 C
ATOM 9 N9 A A 1 14.110 28.394 18.239 1.00 12.71 N
ATOM 10 C8 A A 1 14.042 27.022 18.303 1.00 12.71 C
ATOM 11 N7 A A 1 15.209 26.441 18.421 1.00 12.71 N
ATOM 12 C5 A A 1 16.108 27.492 18.445 1.00 12.71 C
ATOM 13 C6 A A 1 17.508 27.532 18.529 1.00 12.71 C
ATOM 14 N6 A A 1 18.280 26.438 18.548 1.00 12.71 N
ATOM 15 N1 A A 1 18.103 28.749 18.568 1.00 12.71 N
ATOM 16 C2 A A 1 17.332 29.837 18.483 1.00 12.71 C
ATOM 17 N3 A A 1 16.004 29.927 18.368 1.00 12.71 N
ATOM 18 C4 A A 1 15.445 28.706 18.358 1.00 12.71 C

I have posted a picture of the representation at:

http://linegli.mc.vanderbilt.edu/~sabuj/1gqu.png

Is it currently possible to somehow have the base planes on the terminal
adenines (or any other bases) filled in with a color without modifying the pdb?

Thanks,
Sabuj