Also, does the resolution of your data warrant including the hydrogens
in the model ? Can you actually see them ?
You can add them in their riding positions, which may help stablise
your refinement, but not write them out to the coordinate file (uncheck
"and output to coordinate file in the GUI").
Iain
CK wrote:
Hi all,
I am refining a structure that contains RNA. I've added hydrogens
in the riding positions to help with maintaining proper geometry
during refinement. However, when I go to adjust the model between
refinements in coot using Real Space Refine (or even Regularize for
that matter) the RNA "explodes" with atoms going every which way.
This didn't happen before I had added in hydrogens (with Molprobity
via Reduce). Also, when I Real Space Refine residues from the protein
portion, the heavy atoms (C, O, N) behave normally while about half of
the riding hydrogens go wandering off. Any particular reason why this
might be happening?
some (possibly) relevant info:
Platform: Mac PPC-quad running Leopard 10.5.6
Coot 0.6-pre-1 (revision 1941) installed via fink
examples of both protein and RNA from my PDB file:
ATOM 4982 CB ARG D 289 16.348 55.471 6.150 1.00
50.50 A C
ATOM 4983 CG ARG D 289 16.157 54.082 6.707 1.00
49.59 A C
ATOM 4984 CD ARG D 289 15.289 53.235 5.789 1.00
45.31 A C
ATOM 4985 NE ARG D 289 14.871 52.005 6.459 1.00
70.28 A N
ATOM 4986 CZ ARG D 289 13.948 51.167 5.994 1.00
68.12 A C
ATOM 4987 NH1 ARG D 289 13.333 51.422 4.845 1.00
57.79 A N
ATOM 4988 NH2 ARG D 289 13.635 50.075 6.683 1.00
58.77 A N
ATOM 4989 C ARG D 289 17.626 55.916 8.282 1.00
63.79 A C
ATOM 4990 O ARG D 289 17.124 55.238 9.181 1.00
77.16 A O
ATOM 4991 H ARG D 289 17.427 57.565 5.656 0.00
71.69 A H
ATOM 4992 HA ARG D 289 15.928 56.857 7.608 0.00
59.59 A H
ATOM 4993 HB2 ARG D 289 15.511 55.741 5.741 0.00
52.02 A H
ATOM 4994 HB3 ARG D 289 17.041 55.423 5.474 0.00
52.02 A H
ATOM 4995 HG2 ARG D 289 17.021 53.649 6.795 0.00
49.34 A H
ATOM 4996 HG3 ARG D 289 15.720 54.140 7.572 0.00
49.34 A H
ATOM 4997 HD2 ARG D 289 14.495 53.735 5.544 0.00
44.19 A H
ATOM 4998 HD3 ARG D 289 15.795 52.996 4.997 0.00
44.19 A H
ATOM 4999 HE ARG D 289 15.296 51.784 7.302 0.00
71.47 A H
ATOM 5000 HH11 ARG D 289 13.533 52.129 4.398 0.00
56.48 A H
ATOM 5001 HH12 ARG D 289 12.737 50.879 4.547 0.00
56.48 A H
ATOM 5002 HH21 ARG D 289 14.031 49.907 7.428 0.00
59.45 A H
ATOM 5003 HH22 ARG D 289 13.039 49.533 6.382 0.00
59.45 A H
ATOM 8005 P Ar E 18 -9.125 47.764 17.588 1.00
42.70 P
ATOM 8006 OP1 Ar E 18 -10.280 48.637 17.912 1.00
56.33 O
ATOM 8007 OP2 Ar E 18 -7.986 48.283 16.807 1.00
44.20 O
ATOM 8008 O5' Ar E 18 -8.438 47.153 18.884 1.00
45.30 O
ATOM 8009 C5' Ar E 18 -9.198 46.485 19.855 1.00
41.29 C
ATOM 8010 C4' Ar E 18 -8.249 46.040 20.947 1.00
41.68 C
ATOM 8011 O4' Ar E 18 -7.335 45.058 20.393 1.00
43.54 O
ATOM 8012 C1' Ar E 18 -6.142 45.087 21.145 1.00
39.98 C
ATOM 8013 N9 Ar E 18 -5.085 45.353 20.198 1.00
36.77 N
ATOM 8014 C8 Ar E 18 -5.218 45.960 18.981 1.00
40.28 C
ATOM 8015 N7 Ar E 18 -4.088 46.077 18.329 1.00
33.42 N
ATOM 8016 C5 Ar E 18 -3.170 45.501 19.188 1.00
36.92 C
ATOM 8017 C4 Ar E 18 -3.763 45.050 20.351 1.00
39.55 C
ATOM 8018 N3 Ar E 18 -3.176 44.445 21.399 1.00
39.05 N
ATOM 8019 C2 Ar E 18 -1.869 44.309 21.175 1.00
49.05 C
ATOM 8020 N1 Ar E 18 -1.153 44.693 20.098 1.00
55.85 N
ATOM 8021 C6 Ar E 18 -1.786 45.304 19.067 1.00
50.71 C
ATOM 8022 N6 Ar E 18 -1.121 45.704 17.978 1.00
47.54 N
ATOM 8023 C2' Ar E 18 -6.302 46.174 22.196 1.00
39.53 C
ATOM 8024 O2' Ar E 18 -6.816 45.637 23.390 1.00
45.42 O
ATOM 8025 C3' Ar E 18 -7.295 47.092 21.504 1.00
43.28 C
ATOM 8026 O3' Ar E 18 -7.903 48.019 22.406 1.00
47.60 O
ATOM 8027 H5' Ar E 18 -9.636 45.704 19.455 0.00
40.96 H
ATOM 8028 H5'' Ar E 18 -9.872 47.091 20.226 0.00
40.96 H
ATOM 8029 H4' Ar E 18 -8.758 45.636 21.681 0.00
37.61 H
ATOM 8030 H3' Ar E 18 -6.856 47.571 20.770 0.00
42.61 H
ATOM 8031 H2' Ar E 18 -5.451 46.634 22.354 0.00
41.95 H
ATOM 8032 HO2' Ar E 18 -6.956 44.674 23.272 0.00
45.81 H
ATOM 8033 HO3' Ar E 18 -7.578 48.090 23.328 0.00
44.87 H
ATOM 8034 H1' Ar E 18 -5.997 44.219 21.577 0.00
38.30 H
ATOM 8035 H8 Ar E 18 -6.075 46.284 18.633 0.00
41.11 H
ATOM 8036 H61 Ar E 18 -0.154 45.557 17.913 0.00
49.97 H
ATOM 8037 H62 Ar E 18 -1.600 46.145 17.245 0.00
49.97 H
ATOM 8038 H2 Ar E 18 -1.359 43.876 21.891 0.00
50.28 H
Thanks,
Chris K
