Dictionary Bug Fixes - The list and description of fixed bugs

Record of bug fixes for dictionary started from the version 5.32

Entry names Description Fixer Version
H5'' etc in RNA/DAN Hydrogen atoms were H5'1 and H5'2. In new pdb edition it their names are H5' and H5''. This version is compliant with new pdb Many users 5.41
EPE Nitrogen atoms were sp2. They should be sp3 Many use
0D1 This entry was not in the dictionary. R.Joosten 5.39
HEA Sometimes pdb file has atom names N_A, N_B etc and refmac could not read them. These atoms' names in the dictionary are NA, NB etc. Now there are synonyms to deal with this. Kunio
PER Oxygen-oxygen bond in peroxide ion was very short (1.08 - clearly wrong). Now it is 1.462 which is close to values from COD Kunio
EPE There was a chirality that should have not be there. - 5.38
CSI Some atoms were missing and geometry was not good R.Joosten
DAU Atom naming problem R.Joosten
JHZ, B49 Inconsistent atom naming. PDB and dictionary had different names R.Joosten
NDU Problem with atoms O51, O52. Refmac would convert them to OP1, OP2 and then complain. There was a hard coded piece in the program (it was too clever) T.Joosten
mon_lib_list global did not have undescore and one # sign was missing. Don't ask why. P.Emsley after phenixbb discussion. The fix was suggested by D.Radianov
MMA There was a problem with atom name synonyms. Atom C7 was replaced by CM and it caused problem F.Frolov 5.37
OXY The oxygen-oxygen bond length was 1.08. It is now 1.21 as it should be R.Steiner 5.36
EPE Sulphate group was protonated. Now it is fixed B. Lohkamp
UMP It was declared as RNA, however it should be as a free floating monomer R.Joosten
LBV There were som problems with atom names. Robbie Joosten 5.34
NPI Atom names were not consistent with PDB v3 R.Joosten
CPT There were problems with PT. The have been changed now Garib Murshudov 5.34
ADX and ANX There was some problems with protonated oxygens on phosphate groups. P-O bonds have delocalised electrons Bernhard Lohkamp 5.33