From 39f89c287e364aa2e8b0bee51c85a0fca51aa297 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 10 May 2011 16:24:12 +0200
Subject: [PATCH] Just fixed a few spell-os in the tutorial.
---
modules/doc/intro-01.rst | 14 +++++++-------
modules/doc/intro-02.rst | 10 +++++-----
modules/doc/intro-03.rst | 4 ++--
modules/doc/intro.rst | 2 +-
4 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/modules/doc/intro-01.rst b/modules/doc/intro-01.rst
index cca9e786b..8534e9b55 100644
--- a/modules/doc/intro-01.rst
+++ b/modules/doc/intro-01.rst
@@ -10,11 +10,11 @@ The code to load and save structures is not directly part of the mol module, but
:mod:`~ost.io` module. We will be using functions of this module to load
structures.
-One of the most commonly used file formats for macromolecular structures are PDB
-(Brookhaven Protein Databank) files. The official name for molecules stored in
-a PDB file is an *entity* and we decided to follow this convention in
-OpenStructure. You will hear this word all the time, but you can replace the
-word entity with molecule (or most of the time even protein) in your head.
+One of the most commonly used file formats for macromolecular structures are
+PDB (Brookhaven Protein Data Bank) files. The official name for molecules
+stored in a PDB file is an *entity* and we decided to follow this convention
+in OpenStructure. You will hear this word all the time, but you can replace
+the word entity with molecule (or most of the time even protein) in your head.
To load a PDB file, simply type
@@ -95,7 +95,7 @@ of the entity. The graphical representation is completely separate from the :cla
Now you will see the fragment in the 3D window.
-Use the mouse to rotate, zoom in an shift the camera. Double clicking on an
+Use the mouse to rotate, zoom in and shift the camera. Double clicking on an
atom will center the camera on that atom. If you want to learn more about the
:mod:`~ost.gfx` module, you are encouraged to read :doc:`the gfx
intro<intro-03>` and the :mod:`gfx documentation<ost.gfx`.
@@ -106,7 +106,7 @@ Introduction to Views
Often during processing and visualisation of data, only parts of a protein
structure are of interest. This realisation has had a major impact on the design
of OpenStructure and is tied very deeply into the core of the framework.
-Subparts of structure are modeled as so-called :class:`EntityViews
+Subparts of structure are modelled as so-called :class:`EntityViews
<ost.mol.EntityView>`. You can think of them as a selection of chains, residues,
atoms and bonds of an entity. A views has almost the same interface as the
underlying entity, making it very easy to mix entity views with handles in
diff --git a/modules/doc/intro-02.rst b/modules/doc/intro-02.rst
index 95112b0bc..7dbd61172 100644
--- a/modules/doc/intro-02.rst
+++ b/modules/doc/intro-02.rst
@@ -7,7 +7,7 @@ For the course of this tutorial, we assume that you have :ref:`DNG up and runnin
Loading Images and Density Maps
--------------------------------------------------------------------------------
-Openstructure features a :mod:`~ost.img` module that is dedicated to the
+OpenStructure features a :mod:`~ost.img` module that is dedicated to the
manipulation of images/density maps. The images or density maps can either be
one-, two- or three-dimensional. The most common formats used in X-ray and
electron crystallography and atomic force microscope are supported in addition
@@ -20,7 +20,7 @@ To load a density map, type
.. code-block:: python
- map=io.LoadImage('/path/to/examples/map/1ppt.map')
+ map=io.LoadImage('/path/to/examples/code_fragments/map/1ppt.map')
This will load the fragment density map from the specified file 'fragment.map'
and store the result in map.
@@ -31,7 +31,7 @@ Now let's inspect what we just loaded:
print map.GetPixelSampling(), map.GetSize()
-We can see that the sampling is set to 1.0 Angstroems in all three dimensions. The loaded map is an instance of :class:`~ost.img.ImageHandle`, a class to represent images in 1, 2 and 3 dimensions.
+We can see that the sampling is set to 1.0 Angstroms in all three dimensions. The loaded map is an instance of :class:`~ost.img.ImageHandle`, a class to represent images in 1, 2 and 3 dimensions.
Manipulating Images and Density Maps
--------------------------------------------------------------------------------
@@ -47,13 +47,13 @@ first have to import the :mod:`img.alg <ost.img.alg>` module.
The :mod:`img.alg <ost.img.alg>` module provides a wide range of algorithm to
manipulate image data. Here for example we use a LowPassFilter to restrict the
-resolution of the density map to frequencies lower than a treshold.
+resolution of the density map to frequencies lower than a threshold.
.. code-block:: python
map_filtered=map.Apply(alg.LowPassFilter(3.0))
-The filtered map is stored in a new variable called `fragment_map_filtered`. A complete list of algorithms is available on the :doc:`img/alg/alg` page.
+The filtered map is stored in a new variable called `map_filtered`. A complete list of algorithms is available on the :doc:`img/alg/alg` page.
Displaying Images and Density Maps
diff --git a/modules/doc/intro-03.rst b/modules/doc/intro-03.rst
index be0d793b0..8c464e058 100644
--- a/modules/doc/intro-03.rst
+++ b/modules/doc/intro-03.rst
@@ -142,7 +142,7 @@ molecule. This storage scheme has one drawback. Consider the following code:
for i in range(100):
obj.SetColor(gfx.RED)
-While the code obviously achieves the desired effect, it is far for optimal
+While the code obviously achieves the desired effect, it is far from optimal
because all of the 100 color operations are applied every time the graphical
entity needs an update. When you see a slow down in rendering after playing
around with the coloring operations, consider calling
@@ -176,4 +176,4 @@ elements. The main color affects the top and bottom of extended and the outside
of helical elements. The detail color is used for the inner side of helices and
the rim of extended elements. This color is changed with
:meth:`Entity.SetDetailColor`.
-
\ No newline at end of file
+
diff --git a/modules/doc/intro.rst b/modules/doc/intro.rst
index 03bb173c6..c00c465f0 100644
--- a/modules/doc/intro.rst
+++ b/modules/doc/intro.rst
@@ -36,7 +36,7 @@ that comes with OpenStructure. Depending on your platform, the examples are
located at a different location:
* on *MacOS X* the files are located inside the application bundle. The file
- browser fill automatically point to the examples.
+ browser will automatically point to the examples.
* on *Linux* and *Windows* PREFIX/share/openstructure/examples, where PREFIX is
the path to the directory containing OpenStructure.
--
GitLab