VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 15 2004 - 14:38:30 CDT

Hi,
  Thanks for the email. I'll check into this. There could be several
reasons that those residues aren't getting their planes drawn. I suspect
that that there's some very minor thing preventing the Ribbons code from
recognizing those as a candidate for a base plane. Even something as simple
as the particular atom names could do it, or perhaps a minor logic bug.
I looked into it a bit yesterday but I haven't found the exact cause yet.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 14, 2004 at 01:30:18PM -0500, Pattanayek, Sabuj wrote:
> 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 

-- 
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