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<span class="large">Dictionary Bug Fixes</span> - The list and description of fixed bugs
<br /><br />
<p> Record of bug fixes for dictionary started from the version 5.32</p>
<table border=1>
<tr>
<th> Entry names </th>
<th> Description </th>
<th> Fixer </th>
<th> Version </th>
</tr>
<tr>
<td> CPI </td>
<td> This entry had wrong atoms names. It has now been fixed </td>
<td> R.Joosten </td>
<td rowspan=1> 5.41 </td>
</tr>
<tr>
<td> QPT </td>
<td> This entry was not in the dictionary. </td>
<td> R.Joosten </td>
<td rowspan=4> 5.40 </td>
</tr>
<tr>
<td> LNR </td>
<td> Atom naming problem </td>
<td> R.Joosten </td>
</tr>
<tr>
<td> T55 </td>
<td> Atom naming problem </td>
<td> R.Joosten </td>
</tr>
<tr>
<td> 646 </td>
<td> Atom naming problem </td>
<td> R.Joosten </td>
</tr>
<tr>
<td> 0D1 </td>
<td> This entry was not in the dictionary. </td>
<td> R.Joosten </td>
<td rowspan=3> 5.39 </td>
</tr>
<tr>
<td> HEA </td>
<td> 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. </td>
<td> Kunio </td>
</tr>
<tr>
<td> PER </td>
<td> 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 </td>
<td> Kunio </td>
</tr>
<tr>
<td> EPE </td>
<td> There was a chirality that should have not be there. </td>
<td> - </td>
<td rowspan=6> 5.38 </td>
</tr>
<tr>
<td> CSI </td>
<td> Some atoms were missing and geometry was not good </td>
<td> R.Joosten </td>
</tr>
<tr>
<td> DAU </td>
<td> Atom naming problem </td>
<td> R.Joosten </td>
</tr>
<tr>
<td> JHZ, B49 </td>
<td> Inconsistent atom naming. PDB and dictionary had different names </td>
<td> R.Joosten </td>
</tr>
<tr>
<td> NDU </td>
<td> 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) </td>
<td> T.Joosten </td>
</tr>
<tr>
<td> mon_lib_list </td>
<td> global did not have undescore and one # sign was missing. Don't ask why. </td>
<td> P.Emsley after phenixbb discussion. The fix was suggested by D.Radianov </td>
</tr>
<tr>
<td> MMA </td>
<td> There was a problem with atom name synonyms. Atom C7 was replaced by CM and it caused problem </td>
<td> F.Frolov </td>
<td rowspan=1> 5.37 </td>
</tr>
<tr>
<td> OXY </td>
<td> The oxygen-oxygen bond length was 1.08. It is now 1.21 as it should be </td>
<td> R.Steiner </td>
<td rowspan=3> 5.36 </td>
</tr>
<tr>
<td> EPE </td>
<td> Sulphate group was protonated. Now it is fixed </td>
<td> B. Lohkamp </td>
</tr>
<tr>
<td> UMP </td>
<td> It was declared as RNA, however it should be as a free floating monomer </td>
<td> R.Joosten </td>
</tr>
<tr>
<td> LBV </td>
<td> There were som problems with atom names. </td>
<td> Robbie Joosten </td>
<td rowspan=2> 5.34 </td>
</tr>
<tr>
<td> NPI </td>
<td> Atom names were not consistent with PDB v3 </td>
<td> R.Joosten </td>
</tr>
<tr>
<td> CPT </td>
<td> There were problems with PT. The have been changed now </td>
<td> Garib Murshudov </td>
<td> 5.34</td>
<tr>
<td>ADX and ANX</td>
<td> There was some problems with protonated oxygens on phosphate groups. P-O bonds have delocalised electrons</td>
<td> Bernhard Lohkamp</td>
<td> 5.33</td>
</tr>
</table>
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