"nucleic" is based on the residue name being an identified nucleic residue
when there is not other evidence that it is RNA or DNA.
"dna" and "rna" depend upon specific sets of atoms.
In this case, the label "A" identifies these as nucleic, but nothing
identifies them as RNA or DNA.
On Sun, Jun 1, 2014 at 11:16 PM, Eric Martz <[email protected]>
wrote:
> 4olb contains a 9-residue poly-A RNA chain "B". The last 2 residues
> have missing atoms:
>
> REMARK
> 470
> REMARK 470 MISSING
> ATOM
> REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL
> NUMBER;
> REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
> NUMBER;
> REMARK 470 I=INSERTION
> CODE):
> REMARK 470 M RES CSSEQI
> ATOMS
> REMARK 470 A B 8 N9 C8 N7 C5 C6 N6
> N1
> REMARK 470 A B 8 C2 N3
> C4
> REMARK 470 A B 9 C5' C4' O4' C3' O3' C2'
> O2'
> REMARK 470 A B 9 C1' N9 C8 N7 C5 C6
> N6
> REMARK 470 A B 9 N1 C2 N3
> C4
>
>
> ATOM 6537 P A B 8 -34.932 11.724 41.002 1.00
> 77.78 P
> ATOM 6538 OP1 A B 8 -35.604 10.974 42.094 1.00
> 77.35 O
> ATOM 6539 OP2 A B 8 -33.719 12.526 41.308 1.00
> 77.37 O
> ATOM 6540 O5' A B 8 -34.568 10.702 39.831 1.00
> 76.10 O
> ATOM 6541 C5' A B 8 -33.247 10.198 39.673 1.00
> 75.99 C
> ATOM 6542 C4' A B 8 -32.692 10.535 38.309 1.00
> 77.26 C
> ATOM 6543 O4' A B 8 -33.130 11.875 37.967 1.00
> 78.06 O
> ATOM 6544 C3' A B 8 -31.168 10.587 38.180 0.25
> 78.25 C
> ATOM 6545 O3' A B 8 -30.558 9.342 37.861 1.00
> 79.23 O
> ATOM 6546 C2' A B 8 -30.955 11.611 37.072 1.00
> 78.19 C
> ATOM 6547 O2' A B 8 -31.153 11.016 35.797 1.00
> 77.91 O
> ATOM 6548 C1' A B 8 -32.097 12.584 37.326 1.00
> 78.36 C
> ATOM 6549 P A B 9 -30.915 7.974 38.628
> 1.00121.99 P
> ATOM 6550 OP1 A B 9 -32.069 7.374 37.921
> 1.00121.50 O
> ATOM 6551 OP2 A B 9 -30.963 8.222 40.084
> 1.00121.86 O
> ATOM 6552 O5' A B 9 -29.637 7.051 38.359 1.00
> 86.84 O
>
>
> These residues are deemed NOT to be RNA by Jmol (14.0.13, 14.1.16)
>
> load =4olb
> restrict not protein
> selectionhalos on
> select rna
>
> but they are deemed to be "nucleic"
>
> select nucleic
>
> Thus they are nucleic but neither RNA, DNA, nor ligand.
>
>
> *Is this a bug, e.g. undesirable behavior? *Compare with 1bdx which
> contains 64 DNA phosphorus atoms with no other atoms in these residues.
>
> ATOM 1 P DG J 2 37.837 31.943 -10.756 1.00
> 30.00 P
> ATOM 2 P DC J 3 43.246 28.658 -8.793 1.00
> 30.00 P
> ATOM 3 P DA J 4 46.879 26.096 -3.879 1.00
> 30.00 P
> ATOM 4 P DT J 5 47.286 23.980 2.386 1.00
> 30.00 P
> ATOM 5 P DG J 6 44.265 21.858 7.884 1.00
> 30.00 P
>
> Jmol deems these sidechain-less, pentose-less, oxygen-less P atoms to be
> both DNA and nucleic.
>
> load =1bdx
> selectionhalos on
> select dna
> select nucleic
>
> Eric
>
>
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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
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http://p.sf.net/sfu/NeoTech
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