Hi all,
Any idea why my DNA bases will not play nice with Coot's RSR?
error:
click on 2 atoms (in the same molecule)
(4) N1 /1/chainid="D"/9/TD, D occ: 1 with B-factor: 44.27 element: N
at (23.354,31.416,27.363) : 0.112723
(4) N1 /1/chainid="D"/9/TD, D occ: 1 with B-factor: 44.27 element: N
at (23.354,31.416,27.363) : 0.112723
There are 2 data in /sw/share/coot/lib/data/monomers/g/GD.cif
There are 2 data in /sw/share/coot/lib/data/monomers/t/TD.cif
There are 2 data in /sw/share/coot/lib/data/monomers/t/TD.cif
INFO:: 3 residues selected for refined and flanking residues
created 0 bond restraints
created 0 angle restraints
created 0 plane restraints
created 0 chiral vol restraints
created 0 restraints
INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for
link restraints) between (and including) residues 9 and 9 of chain D
Link restraints:
0 bond links
0 angle links
0 plane links
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2
residues (flanking restraints)
a null residue!?
INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2
residues (flanking restraints)
a null residue!?
Flanking residue restraints:
0 flanking bond links
0 flanking angle links
0 flanking torsion links
0 flanking plane links
Refinement elapsed time: 0.057
one of my THY (I changed the resi name to TD and changed the ' to *)
bases:
ATOM 5715 P TD D 9 23.093 30.329 22.069 1.00
43.30 D P
ATOM 5716 O1P TD D 9 24.365 29.595 22.215 1.00
41.18 D O
ATOM 5717 O2P TD D 9 22.690 30.977 20.801 1.00
46.83 D O
ATOM 5718 O5* TD D 9 23.089 31.444 23.211 1.00
41.94 D O
ATOM 5719 N1 TD D 9 23.354 31.416 27.363 1.00
44.27 D N
ATOM 5720 C6 TD D 9 23.937 30.300 26.799 1.00
47.90 D C
ATOM 5721 C2 TD D 9 22.945 31.422 28.680 1.00
45.22 D C
ATOM 5722 O2 TD D 9 22.423 32.384 29.203 1.00
49.38 D O
ATOM 5723 N3 TD D 9 23.162 30.256 29.363 1.00
42.78 D N
ATOM 5724 C4 TD D 9 23.738 29.107 28.862 1.00
49.12 D C
ATOM 5725 O4 TD D 9 23.891 28.109 29.553 1.00
58.02 D O
ATOM 5726 C5 TD D 9 24.143 29.160 27.479 1.00
49.84 D C
ATOM 5727 C5M TD D 9 24.776 27.962 26.839 1.00
53.39 D C
ATOM 5728 C2* TD D 9 24.293 32.982 25.606 1.00
45.99 D C
ATOM 5729 C5* TD D 9 21.971 32.318 23.335 1.00
37.14 D C
ATOM 5730 C4* TD D 9 22.176 33.240 24.520 1.00
40.92 D C
ATOM 5731 O4* TD D 9 22.012 32.481 25.747 1.00
40.44 D O
ATOM 5732 C1* TD D 9 23.152 32.654 26.561 1.00
40.15 D C
ATOM 5733 C3* TD D 9 23.559 33.872 24.604 1.00
40.89 D C
ATOM 5734 O3* TD D 9 23.404 35.176 25.100 1.00
44.90 D O
Thanks,
Scott
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Scott Classen, Ph.D.
SIBYLS Beamline 12.3.1
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Lawrence Berkeley National Laboratory
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