Merge branch 'main' of https://github.com/salilab/imp_spatiotemporal_…

…tutorial
salilab · Dec 4, 2024 · f4b01a1 · f4b01a1
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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/).
-Original file line number
+Diff line change
@@ Expand Up / @@ -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"
        ]
       }
      ],
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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/).