On 06/10/11 15:15, AFL wrote:
Dear All,
I have following definition of ligands in my active site:
ATOM 5137 N1 APPE C 1 -40.239 -29.350 18.293 0.59 8.21
N
ATOM 5138 C2 APPE C 1 -39.254 -30.307 18.165 0.59 10.70
C
ATOM 5139 C2AAPPE C 1 -39.474 -31.666 18.747 0.59 9.96
C
ATOM 5140 C3 APPE C 1 -38.079 -29.961 17.488 0.59 10.13
C
ATOM 5141 O3 APPE C 1 -37.106 -30.887 17.367 0.59 8.86
O
ATOM 5142 C4 APPE C 1 -37.874 -28.683 16.941 0.59 10.62
C
ATOM 5143 C4AAPPE C 1 -36.598 -28.344 16.224 0.59 11.03
C
ATOM 5144 C5 APPE C 1 -38.901 -27.761 17.083 0.59 9.51
C
ATOM 5145 C6 APPE C 1 -40.079 -28.104 17.771 0.59 9.06
C
ATOM 5146 C5AAPPE C 1 -38.837 -26.339 16.571 0.59 9.74
C
ATOM 5147 OP4APPE C 1 -38.192 -25.660 17.528 0.59 11.01
O
ATOM 5148 P APPE C 1 -37.211 -24.252 17.069 0.59 8.36
P
ATOM 5149 OP1APPE C 1 -36.829 -23.753 18.440 0.59 7.37
O
ATOM 5150 OP2APPE C 1 -36.112 -24.904 16.261 0.59 8.91
O
ATOM 5151 OP3APPE C 1 -38.185 -23.407 16.274 0.59 8.73
O
ATOM 5152 NA APPE C 1 -35.911 -29.545 15.698 0.59 22.82
N
ATOM 5153 CAAAPPE C 1 -34.426 -29.329 15.564 0.59 24.98
C
ATOM 5154 CBAAPPE C 1 -33.795 -30.418 14.648 0.59 25.08
C
ATOM 5155 CGAAPPE C 1 -34.787 -30.926 13.587 0.59 28.56
C
ATOM 5156 CDAAPPE C 1 -34.262 -32.127 12.747 0.59 30.07
C
ATOM 5157 OE1APPE C 1 -35.110 -32.856 12.166 0.59 35.08
O
ATOM 5158 OE2APPE C 1 -33.024 -32.329 12.667 0.59 34.57
O
ATOM 5159 CA APPE C 1 -34.098 -27.871 14.984 0.59 25.52
C
ATOM 5160 OA APPE C 1 -33.220 -27.198 15.579 0.59 29.48
O
ATOM 5161 OXTAPPE C 1 -34.725 -27.498 13.981 0.59 24.97
O
TER
ATOM 5162 N BGLU C 1 -35.225 -30.423 13.505 0.41 24.54
N
ATOM 5163 CA BGLU C 1 -34.263 -30.199 14.581 0.41 24.18
C
ATOM 5164 CB BGLU C 1 -32.935 -30.898 14.274 0.41 25.24
C
ATOM 5165 CG BGLU C 1 -31.910 -30.821 15.397 0.41 22.56
C
ATOM 5166 CD BGLU C 1 -31.467 -32.180 15.868 0.41 23.47
C
ATOM 5167 OE1BGLU C 1 -32.350 -32.913 16.366 0.41 10.47
O
ATOM 5168 OE2BGLU C 1 -30.253 -32.504 15.734 0.41 7.74
O
ATOM 5169 C BGLU C 1 -34.037 -28.707 14.797 0.41 24.08
C
ATOM 5170 O BGLU C 1 -33.448 -28.284 15.795 0.41 23.10
O
ATOM 5171 OXTBGLU C 1 -34.462 -27.883 13.984 0.41 27.84
O
TER
When I do real space refinement for the PPE ligand it works fine
(proper cif file is read in beforehand). However, refinement for GLU
fails due to lack of restraints for GLU according to coot. It also fails
when I read in extra cif for GLU myself.
I've tried different naming/numbering schemes for PPE/GLU without success.
One of the problems - perhaps the major one - is that you have two
residues that have the same residue number and chain-id.
So, one of them needs to be changed (to residue 2, say).
Secondly, you have differing alt confs and that is a signal to Coot (at
least) that these residues don't interact - so a PPE-GLU link (if that
is what you are after) will never be made - nor will any non-bonded
interactions.
Thirdly, when Coot tried to make restraints it gives you a "dictionary
problem?" warning - whereas in this case, it is due to an atom selection
problem (no atoms selected).
Paul.
