Re: [phenixbb] hydrogen-bond restraints for Watson-Crick base pairs

Hi Nat, The Ad and * stuff comes from coot OK I renamed all my DNA residues and atom to the PDB version 3 "standard" Ad becomes DA and * becomes ' etc etc. HETATM 1 O5' DA D 1 -47.740 -49.121 -17.972 1.00 91.44 O ANISOU 1 O5' DA D 1 13002 6701 15042 3404 -258 -1747 O HETATM 2 C5' DA D 1 -47.012 -48.219 -17.145 1.00 89.95 C ANISOU 2 C5' DA D 1 12785 6488 14904 3328 -133 -1848 C HETATM 3 C4' DA D 1 -45.570 -48.166 -17.612 1.00 87.82 C ANISOU 3 C4' DA D 1 12704 6315 14346 3354 213 -1700 C HETATM 4 O4' DA D 1 -45.517 -47.624 -18.952 1.00 85.51 O ANISOU 4 O4' DA D 1 12694 6248 13549 3345 56 -1589 O HETATM 5 C3' DA D 1 -44.642 -47.267 -16.812 1.00 88.97 C ANISOU 5 C3' DA D 1 12860 6436 14508 3299 389 -1783 C HETATM 6 O3' DA D 1 -43.312 -47.719 -17.004 1.00 87.64 O ANISOU 6 O3' DA D 1 12793 6290 14216 3376 787 -1645 O HETATM 7 C2' DA D 1 -44.883 -45.902 -17.456 1.00 88.06 C ANISOU 7 C2' DA D 1 12951 6509 13998 3224 84 -1819 C HETATM 8 C1' DA D 1 -45.055 -46.290 -18.922 1.00 86.43 C ANISOU 8 C1' DA D 1 12944 6475 13420 3268 -4 -1650 C HETATM 9 N9 DA D 1 -46.030 -45.477 -19.640 1.00 88.99 N ANISOU 9 N9 DA D 1 13415 6923 13476 3202 -408 -1684 N HETATM 10 C8 DA D 1 -47.262 -45.061 -19.205 1.00 91.41 C ANISOU 10 C8 DA D 1 13632 7157 13943 3159 -766 -1828 C HETATM 11 N7 DA D 1 -47.919 -44.338 -20.086 1.00 91.51 N ANISOU 11 N7 DA D 1 13857 7306 13606 3115 -1076 -1814 N HETATM 12 C5 DA D 1 -47.057 -44.279 -21.180 1.00 89.60 C ANISOU 12 C5 DA D 1 13841 7242 12960 3112 -900 -1656 C HETATM 13 C4 DA D 1 -45.889 -44.979 -20.917 1.00 87.68 C ANISOU 13 C4 DA D 1 13517 6968 12828 3174 -500 -1580 C HETATM 14 N1 DA D 1 -46.108 -43.812 -23.301 1.00 83.38 N ANISOU 14 N1 DA D 1 13478 6809 11393 3063 -789 -1439 N HETATM 15 C2 DA D 1 -45.046 -44.522 -22.903 1.00 82.39 C ANISOU 15 C2 DA D 1 13235 6642 11427 3141 -430 -1387 C HETATM 16 N3 DA D 1 -44.840 -45.143 -21.741 1.00 83.98 N ANISOU 16 N3 DA D 1 13201 6650 12057 3203 -253 -1442 N HETATM 17 C6 DA D 1 -47.151 -43.666 -22.454 1.00 87.19 C ANISOU 17 C6 DA D 1 13821 7135 12171 3057 -1043 -1571 C HETATM 18 N6 DA D 1 -48.209 -42.954 -22.862 1.00 88.07 N Still no luck On Jun 22, 2010, at 3:03 PM, Nathaniel Echols wrote:

On Tue, Jun 22, 2010 at 2:56 PM, Scott Classen wrote: I set main.secondary_structure_restraints = True and it appears that protein ss elements are found and added to the geo file, but watson crick pairs are not.

My DNA looks like this:

HETATM 1 O5* Ad D 1 -47.740 -49.121 -17.972 1.00 91.44 O ANISOU 1 O5* Ad D 1 13002 6701 15042 3404 -258 -1747 O

Is there any reason it wouldn't be recognized by PROBE?

Jeff says that PROBE probably won't recognize "Ad" (it expects "dA" instead), and the default behavior probably requires O5', not O5*. The atom naming we can probably work around, the residue names are more difficult. What program generated these residues?

If you can send us the model (or just enough of it to have base pairs, actually), we'll take a look.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb