Hi all, 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. From the log file: ============================= Secondary structure ============================= No existing secondary structure definitions found. Interpreting HELIX and SHEET records from PDB file Running PROBE to identify base pairs 34 helices and 4 sheets defined 52.1% alpha, 9.0% beta The eff file shows only helix and sheet records and no nucleic_acid records 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 HETATM 2 C5* Ad D 1 -47.012 -48.219 -17.145 1.00 89.95 C ANISOU 2 C5* Ad D 1 12785 6488 14904 3328 -133 -1848 C HETATM 3 C4* Ad D 1 -45.570 -48.166 -17.612 1.00 87.82 C ANISOU 3 C4* Ad D 1 12704 6315 14346 3354 213 -1700 C HETATM 4 O4* Ad D 1 -45.517 -47.624 -18.952 1.00 85.51 O ANISOU 4 O4* Ad D 1 12694 6248 13549 3345 56 -1589 O HETATM 5 C3* Ad D 1 -44.642 -47.267 -16.812 1.00 88.97 C ANISOU 5 C3* Ad D 1 12860 6436 14508 3299 389 -1783 C HETATM 6 O3* Ad D 1 -43.312 -47.719 -17.004 1.00 87.64 O ANISOU 6 O3* Ad D 1 12793 6290 14216 3376 787 -1645 O HETATM 7 C2* Ad D 1 -44.883 -45.902 -17.456 1.00 88.06 C ANISOU 7 C2* Ad D 1 12951 6509 13998 3224 84 -1819 C HETATM 8 C1* Ad D 1 -45.055 -46.290 -18.922 1.00 86.43 C ANISOU 8 C1* Ad D 1 12944 6475 13420 3268 -4 -1650 C HETATM 9 N9 Ad D 1 -46.030 -45.477 -19.640 1.00 88.99 N ANISOU 9 N9 Ad D 1 13415 6923 13476 3202 -408 -1684 N HETATM 10 C8 Ad D 1 -47.262 -45.061 -19.205 1.00 91.41 C ANISOU 10 C8 Ad D 1 13632 7157 13943 3159 -766 -1828 C HETATM 11 N7 Ad D 1 -47.919 -44.338 -20.086 1.00 91.51 N ANISOU 11 N7 Ad D 1 13857 7306 13606 3115 -1076 -1814 N HETATM 12 C5 Ad D 1 -47.057 -44.279 -21.180 1.00 89.60 C ANISOU 12 C5 Ad D 1 13841 7242 12960 3112 -900 -1656 C HETATM 13 C4 Ad D 1 -45.889 -44.979 -20.917 1.00 87.68 C ANISOU 13 C4 Ad D 1 13517 6968 12828 3174 -500 -1580 C HETATM 14 N1 Ad D 1 -46.108 -43.812 -23.301 1.00 83.38 N ANISOU 14 N1 Ad D 1 13478 6809 11393 3063 -789 -1439 N HETATM 15 C2 Ad D 1 -45.046 -44.522 -22.903 1.00 82.39 C ANISOU 15 C2 Ad D 1 13235 6642 11427 3141 -430 -1387 C HETATM 16 N3 Ad D 1 -44.840 -45.143 -21.741 1.00 83.98 N ANISOU 16 N3 Ad D 1 13201 6650 12057 3203 -253 -1442 N HETATM 17 C6 Ad D 1 -47.151 -43.666 -22.454 1.00 87.19 C ANISOU 17 C6 Ad D 1 13821 7135 12171 3057 -1043 -1571 C HETATM 18 N6 Ad D 1 -48.209 -42.954 -22.862 1.00 88.07 N ANISOU 18 N6 Ad D 1 14074 7286 12102 2999 -1409 -1621 N Is there any reason it wouldn't be recognized by PROBE? Thanks, Scott On Jun 22, 2010, at 2:21 PM, Scott Classen wrote:
Hello friendly Phenix developers,
According to the CHANGES for phenix.refine 1.6.2-432 there is a new feature:
"hydrogen-bond restraints for Watson-Crick base pairs"
How do I use this? I couldn't find any documentation... or is it automagic?
Thanks, Scott