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
--- | --- | --- | ---
CPI | This entry had wrong atoms names. It has now been fixed | R.Joosten | 5.41
QPT | This entry was not in the dictionary. | R.Joosten | 5.40
LNR | Atom naming problem | R.Joosten
T55 | Atom naming problem | R.Joosten
646 | Atom naming problem | R.Joosten
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