Give example where we model part of UniProt seq

rnapolii/modeling/.template.deposition.ipynb

@@ -773,10 +773,11 @@
     "(so requires a network connection). Alternatively, we could create ``ihm.reference.UniProtSequence``\n",
     "objects outselves. Here we just populate the first two sequences for illustration.\n",
     "\n",
-    "If for some reason the sequence modeled by IMP is different from that in UniProt, both the alignment\n",
-    "between the two and any single-point mutations should be annotated with ``ihm.reference.Alignment``\n",
-    "and ``ihm.reference.SeqDif`` objects. See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
-    "for an example."
+    "Sometimes the sequence modeled by IMP differs from that in UniProt. In this case the alignment between the two and/or any single-point mutations must be annotated with ``ihm.reference.Alignment`` and ``ihm.reference.SeqDif`` objects:\n",
+    "\n",
+    " - For example, in our modeling of the NPC we only modeled the C-terminal domain of the Nup145 subunit. Thus, the sequence of the Nup145c Entity actually starts at residue 606 in the [UniProt sequence](https://www.uniprot.org/uniprotkb/P49687/entry). See the [NPC scripts](https://github.com/integrativemodeling/npc2018/blob/1299051cf83c3b60514b2f7c1780c60814a3f292/template/1_modeling_wholeNPC.py#L1849-L1868) for an example of creating a suitable Alignment object specifying the offset `db_begin`.\n",
+    " - See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
+    "for an example where the modeled sequence of the RPB5.0 subunit contains four single-point mutations compared to the UniProt sequence P19388."
    ]
   },
   {

rnapolii/modeling/deposition-colab.ipynb

@@ -766,10 +766,11 @@
         "(so requires a network connection). Alternatively, we could create [ihm.reference.UniProtSequence](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.UniProtSequence)\n",
         "objects outselves. Here we just populate the first two sequences for illustration.\n",
         "\n",
-        "If for some reason the sequence modeled by IMP is different from that in UniProt, both the alignment\n",
-        "between the two and any single-point mutations should be annotated with [ihm.reference.Alignment](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.Alignment)\n",
-        "and [ihm.reference.SeqDif](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.SeqDif) objects. See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
-        "for an example."
+        "Sometimes the sequence modeled by IMP differs from that in UniProt. In this case the alignment between the two and/or any single-point mutations must be annotated with [ihm.reference.Alignment](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.Alignment) and [ihm.reference.SeqDif](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.SeqDif) objects:\n",
+        "\n",
+        " - For example, in our modeling of the NPC we only modeled the C-terminal domain of the Nup145 subunit. Thus, the sequence of the Nup145c Entity actually starts at residue 606 in the [UniProt sequence](https://www.uniprot.org/uniprotkb/P49687/entry). See the [NPC scripts](https://github.com/integrativemodeling/npc2018/blob/1299051cf83c3b60514b2f7c1780c60814a3f292/template/1_modeling_wholeNPC.py#L1849-L1868) for an example of creating a suitable Alignment object specifying the offset `db_begin`.\n",
+        " - See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
+        "for an example where the modeled sequence of the RPB5.0 subunit contains four single-point mutations compared to the UniProt sequence P19388."
       ]
     },
     {

rnapolii/modeling/deposition.ipynb

@@ -738,10 +738,11 @@
         "(so requires a network connection). Alternatively, we could create [ihm.reference.UniProtSequence](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.UniProtSequence)\n",
         "objects outselves. Here we just populate the first two sequences for illustration.\n",
         "\n",
-        "If for some reason the sequence modeled by IMP is different from that in UniProt, both the alignment\n",
-        "between the two and any single-point mutations should be annotated with [ihm.reference.Alignment](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.Alignment)\n",
-        "and [ihm.reference.SeqDif](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.SeqDif) objects. See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
-        "for an example."
+        "Sometimes the sequence modeled by IMP differs from that in UniProt. In this case the alignment between the two and/or any single-point mutations must be annotated with [ihm.reference.Alignment](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.Alignment) and [ihm.reference.SeqDif](https://python-ihm.readthedocs.io/en/latest/reference.html#ihm.reference.SeqDif) objects:\n",
+        "\n",
+        " - For example, in our modeling of the NPC we only modeled the C-terminal domain of the Nup145 subunit. Thus, the sequence of the Nup145c Entity actually starts at residue 606 in the [UniProt sequence](https://www.uniprot.org/uniprotkb/P49687/entry). See the [NPC scripts](https://github.com/integrativemodeling/npc2018/blob/1299051cf83c3b60514b2f7c1780c60814a3f292/template/1_modeling_wholeNPC.py#L1849-L1868) for an example of creating a suitable Alignment object specifying the offset `db_begin`.\n",
+        " - See the [pol_ii_g scripts](https://github.com/integrativemodeling/pol_ii_g/blob/a416964fe024352352789d1be8fbd7cfd288832f/production_scripts/sample.py#L288-L305)\n",
+        "for an example where the modeled sequence of the RPB5.0 subunit contains four single-point mutations compared to the UniProt sequence P19388."
       ]
     },
     {