Replace PDBDEV IDs with new PDB IDs and link them

rnapolii/modeling/.template.deposition.ipynb

@@ -1005,10 +1005,10 @@
     "\n",
     "> Note that even though PDB-Dev is still quite small, the models vary widely in composition, e.g.\n",
     ">\n",
-    "> - Some models (e.g. PDBDEV_00000018) are atomic and look much like a traditional \"PDB\" x-ray structure.\n",
-    "> - Some models (e.g. PDBDEV_00000002) contain multiple states that have different sequences (this particular case contains exosome in nucleus-localized and cytoplasm-localized forms).\n",
-    "> - Some models are not of proteins at all - e.g. PDBDEV_00000008 is a model of chromatin, part of the fly genome.\n",
-    "> - Some models contain multiple representations - e.g. PDBDEV_00000012, a model of the yeast nuclear pore complex, contains both models of the scaffold (ring) and the flexible FG repeat regions which occupy the center of the pore.\n",
+    "> - Some models (e.g. [8zzi](https://pdb-dev.wwpdb.org/entry.html?8ZZI)) are atomic and look much like a traditional \"PDB\" x-ray structure.\n",
+    "> - Some models (e.g. [8zz2](https://pdb-dev.wwpdb.org/entry.html?8ZZ2)) contain multiple states that have different sequences (this particular case contains exosome in nucleus-localized and cytoplasm-localized forms).\n",
+    "> - Some models are not of proteins at all - e.g. [8zz8](https://pdb-dev.wwpdb.org/entry.html?8ZZ8) is a model of chromatin, part of the fly genome.\n",
+    "> - Some models contain multiple representations - e.g. [8zzc](https://pdb-dev.wwpdb.org/entry.html?8ZZC), a model of the yeast nuclear pore complex, contains both models of the scaffold (ring) and the flexible FG repeat regions which occupy the center of the pore.\n",
     "\n",
     "[VMD](http://www.ks.uiuc.edu/Research/vmd/) is also reportedly working on support in their forthcoming 1.9.4 release.\n",
     "\n",

rnapolii/modeling/deposition-colab.ipynb

@@ -998,10 +998,10 @@
         "\n",
         "> Note that even though PDB-Dev is still quite small, the models vary widely in composition, e.g.\n",
         ">\n",
-        "> - Some models (e.g. PDBDEV_00000018) are atomic and look much like a traditional \"PDB\" x-ray structure.\n",
-        "> - Some models (e.g. PDBDEV_00000002) contain multiple states that have different sequences (this particular case contains exosome in nucleus-localized and cytoplasm-localized forms).\n",
-        "> - Some models are not of proteins at all - e.g. PDBDEV_00000008 is a model of chromatin, part of the fly genome.\n",
-        "> - Some models contain multiple representations - e.g. PDBDEV_00000012, a model of the yeast nuclear pore complex, contains both models of the scaffold (ring) and the flexible FG repeat regions which occupy the center of the pore.\n",
+        "> - Some models (e.g. [8zzi](https://pdb-dev.wwpdb.org/entry.html?8ZZI)) are atomic and look much like a traditional \"PDB\" x-ray structure.\n",
+        "> - Some models (e.g. [8zz2](https://pdb-dev.wwpdb.org/entry.html?8ZZ2)) contain multiple states that have different sequences (this particular case contains exosome in nucleus-localized and cytoplasm-localized forms).\n",
+        "> - Some models are not of proteins at all - e.g. [8zz8](https://pdb-dev.wwpdb.org/entry.html?8ZZ8) is a model of chromatin, part of the fly genome.\n",
+        "> - Some models contain multiple representations - e.g. [8zzc](https://pdb-dev.wwpdb.org/entry.html?8ZZC), a model of the yeast nuclear pore complex, contains both models of the scaffold (ring) and the flexible FG repeat regions which occupy the center of the pore.\n",
         "\n",
         "[VMD](http://www.ks.uiuc.edu/Research/vmd/) is also reportedly working on support in their forthcoming 1.9.4 release.\n",
         "\n",

rnapolii/modeling/deposition.ipynb

@@ -970,10 +970,10 @@
         "\n",
         "> Note that even though PDB-Dev is still quite small, the models vary widely in composition, e.g.\n",
         ">\n",
-        "> - Some models (e.g. PDBDEV_00000018) are atomic and look much like a traditional \"PDB\" x-ray structure.\n",
-        "> - Some models (e.g. PDBDEV_00000002) contain multiple states that have different sequences (this particular case contains exosome in nucleus-localized and cytoplasm-localized forms).\n",
-        "> - Some models are not of proteins at all - e.g. PDBDEV_00000008 is a model of chromatin, part of the fly genome.\n",
-        "> - Some models contain multiple representations - e.g. PDBDEV_00000012, a model of the yeast nuclear pore complex, contains both models of the scaffold (ring) and the flexible FG repeat regions which occupy the center of the pore.\n",
+        "> - Some models (e.g. [8zzi](https://pdb-dev.wwpdb.org/entry.html?8ZZI)) are atomic and look much like a traditional \"PDB\" x-ray structure.\n",
+        "> - Some models (e.g. [8zz2](https://pdb-dev.wwpdb.org/entry.html?8ZZ2)) contain multiple states that have different sequences (this particular case contains exosome in nucleus-localized and cytoplasm-localized forms).\n",
+        "> - Some models are not of proteins at all - e.g. [8zz8](https://pdb-dev.wwpdb.org/entry.html?8ZZ8) is a model of chromatin, part of the fly genome.\n",
+        "> - Some models contain multiple representations - e.g. [8zzc](https://pdb-dev.wwpdb.org/entry.html?8ZZC), a model of the yeast nuclear pore complex, contains both models of the scaffold (ring) and the flexible FG repeat regions which occupy the center of the pore.\n",
         "\n",
         "[VMD](http://www.ks.uiuc.edu/Research/vmd/) is also reportedly working on support in their forthcoming 1.9.4 release.\n",
         "\n",