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 |