Merge pull request #40 from jimboid/jimboid-patch-1

Author: jimboid

exercise2.ipynb

@@ -49,7 +49,7 @@
    "source": [
     "As an example, let’s look at a protein-DNA complex, deposited with ID [1t38](https://www.ebi.ac.uk/pdbe/entry/pdb/1T38). This has been solved by crystallography (MX) to a resolution of 3.2Å. \n",
     "If you have Coot installed, launch it and select File → Fetch PDB & Map using EDS … → 1t38   This will download the structure and the experimental map, and load them into Coot. It will also alert you to nomenclature problems (just click Cancel).\n",
-    "Otherwise, follow this [link](https://ccpbiosim.duckdns.org/uglymol/1t38/) to view in Uglymol."
+    "Otherwise, follow this [link](https://www.ccpbiosim.ac.uk/uglymol/1t38/) to view in Uglymol."
    ]
   },
   {
@@ -113,7 +113,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As another example, let's look at the nsp12-nsp7-nsp8 RNA polymerase complex from SARS-CoV-2 determined by cryoEM to an overall resolution of 2.5Å. Load the supplied [coordinate]( https://ccpbiosim.duckdns.org/uglymol/pdb_00007bv2_xyz_v1-0.pdb) file (File → Open Coordinates ...) into Coot, followed by the [map]( https://ccpbiosim.duckdns.org/uglymol/emd_30210.map) file (File → Open Map ...). Note that we are using the original coordinate file deposited to the PDB. This has some problems, which we will look at, but has since been updated in the PDB. If you do not have Coot installed, then follow this [link](https://ccpbiosim.duckdns.org/uglymol/7bv2/) to view in Uglymol."
+    "As another example, let's look at the nsp12-nsp7-nsp8 RNA polymerase complex from SARS-CoV-2 determined by cryoEM to an overall resolution of 2.5Å. Load the supplied [coordinate]( https://www.ccpbiosim.ac.uk/uglymol/pdb_00007bv2_xyz_v1-0.pdb) file (File → Open Coordinates ...) into Coot, followed by the [map]( https://www.ccpbiosim.ac.uk/uglymol/emd_30210.map) file (File → Open Map ...). Note that we are using the original coordinate file deposited to the PDB. This has some problems, which we will look at, but has since been updated in the PDB. If you do not have Coot installed, then follow this [link](https://www.ccpbiosim.ac.uk/uglymol/7bv2/) to view in Uglymol."
    ]
   },
   {
@@ -181,7 +181,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When you have finished analysing this structure, download the revised version which is now the default in the PDB. In Coot, load the latest version of the model (7bv2) with File → Get PDB with Accession Code ... How does this compare with the original coordinate file that we have been looking at? If you are using Uglymol, then use this [link](https://ccpbiosim.duckdns.org/uglymol/upload/) and enter 7bv2 into the query box."
+    "When you have finished analysing this structure, download the revised version which is now the default in the PDB. In Coot, load the latest version of the model (7bv2) with File → Get PDB with Accession Code ... How does this compare with the original coordinate file that we have been looking at? If you are using Uglymol, then use this [link](https://www.ccpbiosim.ac.uk/uglymol/upload/) and enter 7bv2 into the query box."
    ]
   },
   {