PDB-Dev is now PDB-IHM

README.md

@@ -5,7 +5,7 @@
 
 This tutorial covers the procedure for depositing integrative modeling
 studies using [IMP](https://integrativemodeling.org/)
-in the [PDB-Dev database](https://pdb-dev.wwpdb.org/) in mmCIF format.
+in the [PDB-IHM database](https://pdb-ihm.org/) in mmCIF format.
 
 See [the IMP website](https://integrativemodeling.org/tutorials/deposition/)
 for the tutorial text.

rnapolii/modeling/.template.deposition.ipynb

@@ -18,9 +18,9 @@
    "source": [
     "# Introduction {#introduction}\n",
     "\n",
-    "In this tutorial we will introduce the procedure used to deposit integrative modeling studies in the [PDB-Dev](https://pdb-dev.wwpdb.org/) database in mmCIF format.\n",
+    "In this tutorial we will introduce the procedure used to deposit integrative modeling studies in the [PDB-IHM](https://pdb-ihm.org/) database in mmCIF format.\n",
     "\n",
-    "We will demonstrate the procedure using [IMP](https://integrativemodeling.org/) and its PMI module, but the database will accept integrative models from any software, as long as they are compliant mmCIF files (e.g. there are several HADDOCK and Rosetta models already in PDB-Dev)."
+    "We will demonstrate the procedure using [IMP](https://integrativemodeling.org/) and its PMI module, but the database will accept integrative models from any software, as long as they are compliant mmCIF files (e.g. there are several HADDOCK and Rosetta models already in PDB-IHM)."
    ]
   },
   {
@@ -39,9 +39,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Why PDB-Dev? {#whypdbdev}\n",
+    "# Why PDB-IHM? {#whypdbihm}\n",
     "\n",
-    "PDB-Dev is a database run by the wwPDB. It is specifically for the deposition of *integrative* models, i.e. models generated using more than one source of experimental data. (Models that use only one experiment generally go in PDB; models that use no experimental information - theoretical models - go in [ModelArchive](https://www.modelarchive.org/))."
+    "PDB-IHM is a database run by the wwPDB. It is specifically for the deposition of *integrative* models, i.e. models generated using more than one source of experimental data. (Models that use only one experiment generally go in PDB; models that use no experimental information - theoretical models - go in [ModelArchive](https://www.modelarchive.org/))."
    ]
   },
   {
@@ -71,7 +71,7 @@
    "source": [
     "# File format {#fileformat}\n",
     "\n",
-    "The file format used by PDB for deposition of integrative modeling studies is the same [mmCIF format](http://mmcif.wwpdb.org/) that is used for crystal structures, with extensions (the [Integrative/Hybrid Methods (IHM) dictionary](http://mmcif.wwpdb.org/dictionaries/mmcif_ihm.dic/Index/)) to support coarse-grained structures, multiple input experimental data sources, multiple states, multiple scales, and ensembles related by time or other order. Currently, models that are compliant with the IHM dictionary can be deposited in the [PDB-Dev](https://pdb-dev.wwpdb.org/) database.\n",
+    "The file format used by PDB for deposition of integrative modeling studies is the same [mmCIF format](http://mmcif.wwpdb.org/) that is used for crystal structures, with extensions (the [Integrative/Hybrid Methods (IHM) dictionary](http://mmcif.wwpdb.org/dictionaries/mmcif_ihm.dic/Index/)) to support coarse-grained structures, multiple input experimental data sources, multiple states, multiple scales, and ensembles related by time or other order. Currently, models that are compliant with the IHM dictionary can be deposited in the [PDB-IHM](https://pdb-ihm.org/) database.\n",
     "\n",
     "mmCIF is a text format with a well-defined syntax, so in principle files could be generated by hand or with simple scripts. However, it is generally easier to use the existing [python-ihm](https://github.com/ihmwg/python-ihm)\n",
     "library. This stores the same data as in an mmCIF file, but represents it as a set of Python classes, so it is easier to manipulate. IMP includes a copy of the python-ihm library, and uses it internally to read and write mmCIF files.\n",
@@ -1002,14 +1002,14 @@
     "mmCIF files can be viewed in many viewers. However, most viewers do not yet support the integrative modeling extensions, and so may only show the atomic parts of the model (if any). Integrative models can be viewed in\n",
     "[ChimeraX](https://www.rbvi.ucsf.edu/chimerax/) - be sure to use a recent nightly build, and open the file from the ChimeraX command line using the `format ihm` option, e.g. `open rnapolii.cif format ihm`. (If you also want to see any DCD files, add `ensembles true` to the end of your command line to load them and then use the ChimeraX `coordset` command to manipulate the set of coordinates, e.g. `coordset slider #1.3.2`.)\n",
     "\n",
-    "ChimeraX also supports downloading and displaying structures directly from the [PDB-Dev](https://pdb-dev.wwpdb.org/) database, for example from the ChimeraX command line `open 10 from pdbdev`.\n",
+    "ChimeraX also supports downloading and displaying structures directly from the precursor [PDB-Dev](https://pdb-dev.wwpdb.org/) database, for example from the ChimeraX command line `open 10 from pdbdev`.\n",
     "\n",
-    "> Note that even though PDB-Dev is still quite small, the models vary widely in composition, e.g.\n",
+    "> Note that even though PDB-IHM is still quite small, the models vary widely in composition, e.g.\n",
     ">\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",
+    "> - Some models (e.g. [8zzi](https://pdb-ihm.org/entry.html?8ZZI)) are atomic and look much like a traditional \"PDB\" x-ray structure.\n",
+    "> - Some models (e.g. [8zz2](https://pdb-ihm.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-ihm.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-ihm.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",
@@ -1085,7 +1085,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Similarly we could explore any integrative model deposited in PDB-Dev. For example we can look at PDB-Dev \\#14, a [HADDOCK](http://www.bonvinlab.org/software/haddock2.2/) model:"
+    "Similarly we could explore any integrative model deposited in PDB-IHM. For example we can look at PDB entry 8ZZE, a [HADDOCK](http://www.bonvinlab.org/software/haddock2.2/) model:"
    ]
   },
   {
@@ -1099,7 +1099,7 @@
     "except ImportError:\n",
     "    import urllib2  # python2\n",
     "\n",
-    "fh = urllib2.urlopen('https://pdb-dev.wwpdb.org/cif/8zze.cif')\n",
+    "fh = urllib2.urlopen('https://pdb-ihm.org/cif/8zze.cif')\n",
     "s, = ihm.reader.read(fh)\n",
     "print(s.title, s.restraints, s.ensembles, s.state_groups)"
    ]

rnapolii/modeling/deposition-colab.ipynb

@@ -11,7 +11,7 @@
         "**Table of contents**\n",
         "\n",
         " - [Introduction](#introduction)\n",
-        " - [Why PDB-Dev?](#whypdbdev)\n",
+        " - [Why PDB-IHM?](#whypdbihm)\n",
         " - [Why mmCIF?](#whymmcif)\n",
         " - [Study versus single model](#studyvmodel)\n",
         " - [File format](#fileformat)\n",
@@ -40,18 +40,18 @@
       "source": [
         "# Introduction<a id=\"introduction\"></a>\n",
         "\n",
-        "In this tutorial we will introduce the procedure used to deposit integrative modeling studies in the [PDB-Dev](https://pdb-dev.wwpdb.org/) database in mmCIF format.\n",
+        "In this tutorial we will introduce the procedure used to deposit integrative modeling studies in the [PDB-IHM](https://pdb-ihm.org/) database in mmCIF format.\n",
         "\n",
-        "We will demonstrate the procedure using [IMP](https://integrativemodeling.org/) and its PMI module, but the database will accept integrative models from any software, as long as they are compliant mmCIF files (e.g. there are several HADDOCK and Rosetta models already in PDB-Dev)."
+        "We will demonstrate the procedure using [IMP](https://integrativemodeling.org/) and its PMI module, but the database will accept integrative models from any software, as long as they are compliant mmCIF files (e.g. there are several HADDOCK and Rosetta models already in PDB-IHM)."
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "# Why PDB-Dev?<a id=\"whypdbdev\"></a>\n",
+        "# Why PDB-IHM?<a id=\"whypdbihm\"></a>\n",
         "\n",
-        "PDB-Dev is a database run by the wwPDB. It is specifically for the deposition of *integrative* models, i.e. models generated using more than one source of experimental data. (Models that use only one experiment generally go in PDB; models that use no experimental information - theoretical models - go in [ModelArchive](https://www.modelarchive.org/))."
+        "PDB-IHM is a database run by the wwPDB. It is specifically for the deposition of *integrative* models, i.e. models generated using more than one source of experimental data. (Models that use only one experiment generally go in PDB; models that use no experimental information - theoretical models - go in [ModelArchive](https://www.modelarchive.org/))."
       ]
     },
     {
@@ -81,7 +81,7 @@
       "source": [
         "# File format<a id=\"fileformat\"></a>\n",
         "\n",
-        "The file format used by PDB for deposition of integrative modeling studies is the same [mmCIF format](http://mmcif.wwpdb.org/) that is used for crystal structures, with extensions (the [Integrative/Hybrid Methods (IHM) dictionary](http://mmcif.wwpdb.org/dictionaries/mmcif_ihm.dic/Index/)) to support coarse-grained structures, multiple input experimental data sources, multiple states, multiple scales, and ensembles related by time or other order. Currently, models that are compliant with the IHM dictionary can be deposited in the [PDB-Dev](https://pdb-dev.wwpdb.org/) database.\n",
+        "The file format used by PDB for deposition of integrative modeling studies is the same [mmCIF format](http://mmcif.wwpdb.org/) that is used for crystal structures, with extensions (the [Integrative/Hybrid Methods (IHM) dictionary](http://mmcif.wwpdb.org/dictionaries/mmcif_ihm.dic/Index/)) to support coarse-grained structures, multiple input experimental data sources, multiple states, multiple scales, and ensembles related by time or other order. Currently, models that are compliant with the IHM dictionary can be deposited in the [PDB-IHM](https://pdb-ihm.org/) database.\n",
         "\n",
         "mmCIF is a text format with a well-defined syntax, so in principle files could be generated by hand or with simple scripts. However, it is generally easier to use the existing [python-ihm](https://github.com/ihmwg/python-ihm)\n",
         "library. This stores the same data as in an mmCIF file, but represents it as a set of Python classes, so it is easier to manipulate. IMP includes a copy of the python-ihm library, and uses it internally to read and write mmCIF files.\n",
@@ -995,14 +995,14 @@
         "mmCIF files can be viewed in many viewers. However, most viewers do not yet support the integrative modeling extensions, and so may only show the atomic parts of the model (if any). Integrative models can be viewed in\n",
         "[ChimeraX](https://www.rbvi.ucsf.edu/chimerax/) - be sure to use a recent nightly build, and open the file from the ChimeraX command line using the `format ihm` option, e.g. `open rnapolii.cif format ihm`. (If you also want to see any DCD files, add `ensembles true` to the end of your command line to load them and then use the ChimeraX `coordset` command to manipulate the set of coordinates, e.g. `coordset slider #1.3.2`.)\n",
         "\n",
-        "ChimeraX also supports downloading and displaying structures directly from the [PDB-Dev](https://pdb-dev.wwpdb.org/) database, for example from the ChimeraX command line `open 10 from pdbdev`.\n",
+        "ChimeraX also supports downloading and displaying structures directly from the precursor [PDB-Dev](https://pdb-dev.wwpdb.org/) database, for example from the ChimeraX command line `open 10 from pdbdev`.\n",
         "\n",
-        "> Note that even though PDB-Dev is still quite small, the models vary widely in composition, e.g.\n",
+        "> Note that even though PDB-IHM is still quite small, the models vary widely in composition, e.g.\n",
         ">\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",
+        "> - Some models (e.g. [8zzi](https://pdb-ihm.org/entry.html?8ZZI)) are atomic and look much like a traditional \"PDB\" x-ray structure.\n",
+        "> - Some models (e.g. [8zz2](https://pdb-ihm.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-ihm.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-ihm.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",
@@ -1078,7 +1078,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Similarly we could explore any integrative model deposited in PDB-Dev. For example we can look at PDB-Dev \\#14, a [HADDOCK](http://www.bonvinlab.org/software/haddock2.2/) model:"
+        "Similarly we could explore any integrative model deposited in PDB-IHM. For example we can look at PDB entry 8ZZE, a [HADDOCK](http://www.bonvinlab.org/software/haddock2.2/) model:"
       ]
     },
     {
@@ -1092,7 +1092,7 @@
         "except ImportError:\n",
         "    import urllib2  # python2\n",
         "\n",
-        "fh = urllib2.urlopen('https://pdb-dev.wwpdb.org/cif/8zze.cif')\n",
+        "fh = urllib2.urlopen('https://pdb-ihm.org/cif/8zze.cif')\n",
         "s, = ihm.reader.read(fh)\n",
         "print(s.title, s.restraints, s.ensembles, s.state_groups)"
       ]