From 09aa1146d87ec85c853055870521aff23e6e364d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 27 Aug 2024 11:04:56 -0700 Subject: [PATCH] Replace PDBDEV IDs with new PDB IDs and link them --- rnapolii/modeling/.template.deposition.ipynb | 8 ++++---- rnapolii/modeling/deposition-colab.ipynb | 8 ++++---- rnapolii/modeling/deposition.ipynb | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/rnapolii/modeling/.template.deposition.ipynb b/rnapolii/modeling/.template.deposition.ipynb index 443d546..9545d05 100644 --- a/rnapolii/modeling/.template.deposition.ipynb +++ b/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", diff --git a/rnapolii/modeling/deposition-colab.ipynb b/rnapolii/modeling/deposition-colab.ipynb index f7f1ce7..49b3f15 100644 --- a/rnapolii/modeling/deposition-colab.ipynb +++ b/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", diff --git a/rnapolii/modeling/deposition.ipynb b/rnapolii/modeling/deposition.ipynb index 0b1a686..071f45b 100644 --- a/rnapolii/modeling/deposition.ipynb +++ b/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",