From 0bdc14847953c79e6e7221ddd904846d8a7d2ec9 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Tue, 3 Dec 2024 14:47:38 -0800
Subject: [PATCH] PDB-Dev is now PDB-IHM

---
 Jupyter/.template.spatiotemporal.ipynb | 2 +-
 Jupyter/html/notebook.html             | 2 +-
 Jupyter/spatiotemporal-colab.ipynb     | 2 +-
 Jupyter/spatiotemporal.ipynb           | 2 +-
 doc/trajectory.md                      | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Jupyter/.template.spatiotemporal.ipynb b/Jupyter/.template.spatiotemporal.ipynb
index c39009d4f..3d2fa2f50 100644
--- a/Jupyter/.template.spatiotemporal.ipynb
+++ b/Jupyter/.template.spatiotemporal.ipynb
@@ -1281,7 +1281,7 @@
     "\n",
     "After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The [integrative spatiotemporal modeling procedure](https://integrativemodeling.org/tutorials/spatiotemporal/index.html#steps) can then be repeated iteratively, analogous to [integrative modeling of static structures](https://integrativemodeling.org/2.21.0/doc/manual/intro.html#procedure).\n",
     "\n",
-    "If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-dev database](https://pdb-dev.wwpdb.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).\n"
+    "If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-IHM database](https://pdb-ihm.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).\n"
    ]
   }
  ],
diff --git a/Jupyter/html/notebook.html b/Jupyter/html/notebook.html
index 197d8aeaa..ab14bbdb8 100644
--- a/Jupyter/html/notebook.html
+++ b/Jupyter/html/notebook.html
@@ -992,7 +992,7 @@ <h2><a class="anchor" id="notebook_trajectory_validation"></a>
 <h1><a class="anchor" id="notebook_Conclusion"></a>
 Next steps</h1>
 <p>After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The <a href="https://integrativemodeling.org/tutorials/spatiotemporal/index.html#steps">integrative spatiotemporal modeling procedure</a> can then be repeated iteratively, analogous to <a href="https://integrativemodeling.org/2.21.0/doc/manual/intro.html#procedure">integrative modeling of static structures</a>.</p>
-<p>If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an <a href="https://mmcif.wwpdb.org/">mmCIF file</a> to deposit the model in the <a href="https://pdb-dev.wwpdb.org/">PDB-dev database</a>. This procedure is explained in the <a href="https://integrativemodeling.org/tutorials/deposition/develop/">deposition tutorial</a>. </p>
+<p>If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an <a href="https://mmcif.wwpdb.org/">mmCIF file</a> to deposit the model in the <a href="https://pdb-ihm.org/">PDB-IHM database</a>. This procedure is explained in the <a href="https://integrativemodeling.org/tutorials/deposition/develop/">deposition tutorial</a>. </p>
 </div></div><!-- contents -->
 </div><!-- PageDoc -->
 </div>
diff --git a/Jupyter/spatiotemporal-colab.ipynb b/Jupyter/spatiotemporal-colab.ipynb
index 8e9b5c444..905d274ff 100644
--- a/Jupyter/spatiotemporal-colab.ipynb
+++ b/Jupyter/spatiotemporal-colab.ipynb
@@ -1288,7 +1288,7 @@
     "\n",
     "After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The [integrative spatiotemporal modeling procedure](https://integrativemodeling.org/tutorials/spatiotemporal/index.html#steps) can then be repeated iteratively, analogous to [integrative modeling of static structures](https://integrativemodeling.org/2.21.0/doc/manual/intro.html#procedure).\n",
     "\n",
-    "If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-dev database](https://pdb-dev.wwpdb.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).\n"
+    "If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-IHM database](https://pdb-ihm.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).\n"
    ]
   }
  ],
diff --git a/Jupyter/spatiotemporal.ipynb b/Jupyter/spatiotemporal.ipynb
index c1f58a8d5..5cd82447f 100644
--- a/Jupyter/spatiotemporal.ipynb
+++ b/Jupyter/spatiotemporal.ipynb
@@ -1263,7 +1263,7 @@
     "\n",
     "After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The [integrative spatiotemporal modeling procedure](https://integrativemodeling.org/tutorials/spatiotemporal/index.html#steps) can then be repeated iteratively, analogous to [integrative modeling of static structures](https://integrativemodeling.org/2.21.0/doc/manual/intro.html#procedure).\n",
     "\n",
-    "If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-dev database](https://pdb-dev.wwpdb.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).\n"
+    "If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-IHM database](https://pdb-ihm.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).\n"
    ]
   }
  ],
diff --git a/doc/trajectory.md b/doc/trajectory.md
index 25e3409b9..53d7336d7 100644
--- a/doc/trajectory.md
+++ b/doc/trajectory.md
@@ -266,4 +266,4 @@ Next, we can evaluate the accuracy of the model by comparing the RMSD to the PDB
 
 After assessing our model, we can must decide if the model is sufficient to answer biological questions of interest. If the model does not have sufficient precision for the desired application, assessment of the current model can be used to inform which new experiments may help improve the next iteration of the model. The [integrative spatiotemporal modeling procedure](@ref steps) can then be repeated iteratively, analogous to [integrative modeling of static structures](@ref procedure).
 
-If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-dev database](https://pdb-dev.wwpdb.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).
+If the model is sufficient to provide insight into the biological process of interest, the user may decide that it is ready for publication. In this case, the user should create an [mmCIF file](https://mmcif.wwpdb.org/) to deposit the model in the [PDB-IHM database](https://pdb-ihm.org/). This procedure is explained in the [deposition tutorial](https://integrativemodeling.org/tutorials/deposition/develop/).