diff --git a/_images/51cf05d799f955c6bc97abcf6bfa7eac8bb03bc68d73d250a2960282cbabfdf5.png b/_images/51cf05d799f955c6bc97abcf6bfa7eac8bb03bc68d73d250a2960282cbabfdf5.png deleted file mode 100644 index 80a563e..0000000 Binary files a/_images/51cf05d799f955c6bc97abcf6bfa7eac8bb03bc68d73d250a2960282cbabfdf5.png and /dev/null differ diff --git a/_images/8371472862b2f922bb59a0c77e0921582d686f681160f65fe0c5f8e819d19d96.png b/_images/8371472862b2f922bb59a0c77e0921582d686f681160f65fe0c5f8e819d19d96.png deleted file mode 100644 index 860880a..0000000 Binary files a/_images/8371472862b2f922bb59a0c77e0921582d686f681160f65fe0c5f8e819d19d96.png and /dev/null differ diff --git a/_images/8df5c7f39f20f1dee3db00356185d516ae31773f65ba0ba8861e8f33591effd8.png b/_images/8df5c7f39f20f1dee3db00356185d516ae31773f65ba0ba8861e8f33591effd8.png new file mode 100644 index 0000000..d708bf8 Binary files /dev/null and b/_images/8df5c7f39f20f1dee3db00356185d516ae31773f65ba0ba8861e8f33591effd8.png differ diff --git a/_images/bc36ef4c8e3d0ad87b6d00f65e26fbcc03e4832803205f2b3d8c36c971e45e48.png b/_images/bc36ef4c8e3d0ad87b6d00f65e26fbcc03e4832803205f2b3d8c36c971e45e48.png new file mode 100644 index 0000000..1d00039 Binary files /dev/null and b/_images/bc36ef4c8e3d0ad87b6d00f65e26fbcc03e4832803205f2b3d8c36c971e45e48.png differ diff --git a/chapters/Creating_Plots_in_Jupyter_Notebooks.html b/chapters/Creating_Plots_in_Jupyter_Notebooks.html index 415d59b..a92e1f6 100644 --- a/chapters/Creating_Plots_in_Jupyter_Notebooks.html +++ b/chapters/Creating_Plots_in_Jupyter_Notebooks.html @@ -465,7 +465,7 @@

Using Matplotlib.pyplot
-
<matplotlib.collections.PathCollection at 0x7fec32370310>
+
<matplotlib.collections.PathCollection at 0x7fe8181dcbd0>
 

 

 ../_images/ceaaf9ece89b08454dd7707908e35945d376737045e460c49eebbcadd1df23cf.png
@@ -481,7 +481,7 @@ 
Using Matplotlib.pyplot
-
[<matplotlib.lines.Line2D at 0x7fec3239e310>]
+
[<matplotlib.lines.Line2D at 0x7fe8181e9510>]
 

 

 ../_images/720b0e757eaaa9fb1a4f291e9abd2db1cede159aac7a370b4b02faa4ef0066e2.png
@@ -579,7 +579,7 @@ 
Scatter Plots with Seaborn
<Axes: xlabel='Protein Concentration (mg/mL)', ylabel='A595'>
-../_images/8371472862b2f922bb59a0c77e0921582d686f681160f65fe0c5f8e819d19d96.png +../_images/bc36ef4c8e3d0ad87b6d00f65e26fbcc03e4832803205f2b3d8c36c971e45e48.png
@@ -628,7 +628,7 @@

Scatter Plots with Seaborn -../_images/51cf05d799f955c6bc97abcf6bfa7eac8bb03bc68d73d250a2960282cbabfdf5.png +../_images/8df5c7f39f20f1dee3db00356185d516ae31773f65ba0ba8861e8f33591effd8.png

diff --git a/chapters/MolVis_with_iCN3D.html b/chapters/MolVis_with_iCN3D.html index 7ef7bc0..8228ea0 100644 --- a/chapters/MolVis_with_iCN3D.html +++ b/chapters/MolVis_with_iCN3D.html @@ -424,8 +424,8 @@

Viewing a PDB structure

-
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad347d9850>
+
<icn3dpy.view at 0x7fd36c6d74d0>
@@ -502,8 +502,8 @@

Applying the power of python -
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad346203d0>
+
<icn3dpy.view at 0x7fd36c6f0e90>
@@ -581,8 +581,8 @@

Adding commands to the icn3dpy.view function -
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad3462fe90>
+
<icn3dpy.view at 0x7fd36c6fd910>
@@ -649,8 +649,8 @@

Adding commands to the icn3dpy.view function -
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad34631690>
+
<icn3dpy.view at 0x7fd36c700bd0>
@@ -720,8 +720,8 @@

Adding commands to the icn3dpy.view function -
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad34633dd0>
+
<icn3dpy.view at 0x7fd36c703cd0>
@@ -792,8 +792,8 @@

Adding commands to the icn3dpy.view function -
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad34636250>
+
<icn3dpy.view at 0x7fd36c706110>
@@ -876,8 +876,8 @@

Pulling collections of commands from an iCN3D web page

-
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad34637a50>
+
<icn3dpy.view at 0x7fd36c8a8e10>
@@ -955,8 +955,8 @@

Teasing apart the command set from the -
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad34604dd0>
+
<icn3dpy.view at 0x7fd36c6f4c50>
@@ -1045,8 +1045,8 @@

Creating functions based on preferred command sets generated from iCN3D web

-
-

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
+

+

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the extension:
jupyter labextension install jupyterlab_3dmol

<icn3dpy.view at 0x7fad3461ab90>
+
<icn3dpy.view at 0x7fd36c6e79d0>
diff --git a/chapters/binding_site_investigation.html b/chapters/binding_site_investigation.html index 49ca487..b39e00f 100644 --- a/chapters/binding_site_investigation.html +++ b/chapters/binding_site_investigation.html @@ -470,7 +470,7 @@

View the structure -

+

Text here about NGLView

@@ -481,7 +481,7 @@

View the structure -

+

This view looks a bit messy. MDAnalysis has a human readable selection syntax that allows us to isolate parts of our structure. We will take our MDAnalysis Universe (the variable u) and use the select_atoms function. @@ -505,7 +505,7 @@

View the structure -

+

Upon viewing this structure, you will notice that our ligand seems to appear twice. If you open the PDB file to investigate, you will see the following in the ligand section:

@@ -543,7 +543,7 @@

View the structure -

+

@@ -552,7 +552,7 @@

View the structure -

+

When we inspect the ligand in the binding site, we notice a few things. First, the binding site has a large hydrophobic area on the surface. diff --git a/chapters/nonlinear_regression_part_2.html b/chapters/nonlinear_regression_part_2.html index a8db1cb..a0683db 100644 --- a/chapters/nonlinear_regression_part_2.html +++ b/chapters/nonlinear_regression_part_2.html @@ -557,7 +557,7 @@

The Michaelis-Menten equation -
[<matplotlib.lines.Line2D at 0x7fd8e6db7f10>]
+
[<matplotlib.lines.Line2D at 0x7faf90849450>]
 

 

 ../_images/ed2e8a80cd568b164f79f3c9cf21556ba7d5baac33497c50cc6db1e0744d85e0.png
diff --git a/chapters/rcsb_api.html b/chapters/rcsb_api.html
index aa41116..e3fa203 100644
--- a/chapters/rcsb_api.html
+++ b/chapters/rcsb_api.html
@@ -680,7 +680,7 @@ 
PDB Search API
-
{'query_id': '1a6a7ab9-1503-4a5b-8875-7d29c82bf354',
+
{'query_id': '4a0becaa-d9c8-4f68-9349-29cee744f9a9',
  'result_type': 'entry',
  'total_count': 668,
  'result_set': [{'identifier': '2BMM', 'score': 1.0},
@@ -802,7 +802,7 @@ 
PDB Search API
-
{'query_id': 'a5117d87-a456-41f6-96d7-19fd3e32cbe7',
+
{'query_id': '9d8db27b-ab5f-4204-ab73-d4fddfb36c18',
  'result_type': 'entry',
  'total_count': 571,
  'result_set': [{'identifier': '1MBN', 'score': 1.0},
diff --git a/searchindex.js b/searchindex.js
index bda519a..c032eeb 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1D arrays": [[8, "d-arrays"], [12, "d-arrays"]], "2D arrays": [[8, "id1"], [12, "id1"]], "3D arrays": [[8, "id2"], [12, "id2"]], "A final note about regular expressions": [[2, "a-final-note-about-regular-expressions"]], "A final note about string formatting": [[6, "a-final-note-about-string-formatting"]], "A note about jupyter notebooks": [[11, "a-note-about-jupyter-notebooks"]], "Absolute and relative paths": [[2, "absolute-and-relative-paths"]], "Add the column to the dataframe": [[3, "add-the-column-to-the-dataframe"]], "Adding commands to the icn3dpy.view function": [[5, "adding-commands-to-the-icn3dpy-view-function"]], "Analyzing MMCIF Files using Biopython": [[10, "analyzing-mmcif-files-using-biopython"]], "Answer": [[2, null], [2, null]], "Applying the power of python": [[5, "applying-the-power-of-python"]], "Assigning multiple variables at once": [[11, "assigning-multiple-variables-at-once"]], "Assigning variables and data types": [[11, "assigning-variables-and-data-types"]], "Calculate the Slopes": [[12, "calculate-the-slopes"]], "Calculate the initial velocity": [[12, "calculate-the-initial-velocity"]], "Calculating the initial velocity": [[12, "calculating-the-initial-velocity"]], "Challenge - Repeat analysis for a Zinc Finger": [[10, "challenge-repeat-analysis-for-a-zinc-finger"]], "Check Your Understanding": [[2, null], [2, null], [6, null]], "Check your Understanding": [[0, null], [2, null]], "Check your understanding": [[6, null], [8, null], [11, null], [12, null]], "Common errors": [[13, "common-errors"]], "Converting the 2D ligand structures to 3D structures for use in docking": [[4, "converting-the-2d-ligand-structures-to-3d-structures-for-use-in-docking"]], "Create the Equation": [[3, "create-the-equation"]], "Creating Functions": [[13, "creating-functions"]], "Creating Plots in Jupyter Notebooks": [[0, "creating-plots-in-jupyter-notebooks"]], "Creating functions based on preferred command sets generated 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"extracting-the-output-from-curve-fit"]], "File Download using Biopython": [[14, "file-download-using-biopython"]], "File Parsing": [[2, "file-parsing"]], "Finding information in a dataframe": [[8, "finding-information-in-a-dataframe"]], "Finding the ligands": [[1, "finding-the-ligands"]], "Getting Started": [[11, "getting-started"]], "Hint": [[2, null], [3, null], [6, null], [12, null]], "How do we download the ligand files?": [[1, "how-do-we-download-the-ligand-files"]], "Importing data with pandas": [[3, "importing-data-with-pandas"]], "Importing libraries": [[6, "importing-libraries"]], "Importing python libraries": [[8, "importing-python-libraries"]], "Importing the Data": [[12, "importing-the-data"]], "Importing the data with pandas": [[8, "importing-the-data-with-pandas"]], "Inspect the data": [[12, "inspect-the-data"]], "Install nglview": [[15, "install-nglview"]], "Installing Python through Anaconda": [[15, "installing-python-through-anaconda"]], "Introduction": [[11, 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[[14, "programmatic-access-of-apis"]], "Project": [[6, null]], "Pulling collections of commands from an iCN3D web page": [[5, "pulling-collections-of-commands-from-an-icn3d-web-page"]], "Questions": [[4, "questions"]], "Reading MMCIF Files": [[10, "reading-mmcif-files"]], "Reading a file": [[2, "reading-a-file"]], "Reading multiple files with nested for loops": [[6, "reading-multiple-files-with-nested-for-loops"]], "Repeating an operation many times: for loops": [[11, "repeating-an-operation-many-times-for-loops"]], "Results for Glucose and ATP": [[4, "results-for-glucose-and-atp"]], "Retrieving Information from the PDB using the Web API": [[14, "retrieving-information-from-the-pdb-using-the-web-api"]], "Review of f string printing": [[13, "review-of-f-string-printing"]], "Scatter Plots with Seaborn": [[0, "scatter-plots-with-seaborn"]], "Searching for a particular line number in your file": [[2, "searching-for-a-particular-line-number-in-your-file"]], "Searching for a pattern in your 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