changed warning message, added info about deprecating a crystal

Author: tdudgeon

USER-GUIDE.md

@@ -345,6 +345,22 @@ XCA looks for all `LINK` records, selects only those involving the relevant liga
 example) and grafts the protein atom onto the ligand for each record (of course, usually there will only be a single
 one for each ligand).
 
+#### Overriding status
+
+There is a mechanism to manually override the status of any crystal. Typically you would use this to deprecate a crystal
+that had previously been included, but you now want to exclude from analysis in Fragalysis. To do this add a section like
+this at the top level of your `config.yaml` file:
+
+```yaml
+overrides:
+  crystals:
+    A71EV2A-x0202:
+      status: deprecated
+      status_reason: bad karma
+```
+
+That example would mark the crystal `A71EV2A-x0202` as being of `deprecated` status.
+
 ### 2.3. The assemblies YAML
 
 This file specifies both the biological *assemblies* and *crystalforms* relative to some reference PDBs.

src/xchemalign/aligner.py

@@ -718,9 +718,10 @@ def _perform_alignments(self, meta):
                                     + ligand_residue
                                     + ' in crystal '
                                     + dtag
-                                    + '. '
-                                    + 'Maybe this is caused by the ligand residue number changing between versions. '
-                                    + 'If you can\'t correct this then add this crystal to the \`excludes\` list.'
+                                    + '. One cause for this is the ligand residue number changing between versions;'
+                                    + ' if it\'s not that, the cause might be even more obscure.'
+                                    + ' Talk to a developer, and good luck.'
+                                    + ' If you can\'t correct this then you can add this crystal to the \`exclude\` list.'
                                 )
                                 self._log_error(msg)
                                 exit(1)

src/xchemalign/collator.py

@@ -1212,7 +1212,7 @@ def _munge_history(self, meta):
         new_or_updated_xtals = {}
 
         # get any user defined overrides
-        overrides = self.config.get("overrides", {})
+        overrides = self.config.get(Constants.CONFIG_OVERRIDES, {})
 
         count = 0
         for metad in self.meta_history:

src/xchemalign/utils.py

@@ -62,6 +62,7 @@ class Constants:
     CONFIG_CODE_PREFIX = 'code_prefix'
     CONFIG_CODE_PREFIX_TOOLTIP = 'code_prefix_tooltip'
     CONFIG_PANDDAS_EVENT_FILES = "panddas_event_files"
+    CONFIG_OVERRIDES = "overrides"
     META_RUN_ON = "run_on"
     META_INPUT_DIRS = "input_dirs"
     META_VERSION_NUM = "version_number"