Update README.md

MooersLab · MooersLab · commit 1cb05f03613f · 2016-05-02T21:49:21.000-05:00
diff --git a/README.md b/README.md
@@ -49,7 +49,7 @@ Paste the above reformated [`set_view()`](http://pymolwiki.org/index.php/Set_Vie
 
 ###What is the roundview() function?
 
-The Python script roundview.py includes the function `roundview()` that reformats the viewing port settings from seven rows to one row. The more compact format from roundview() is easy to copy and paste onto the command line. Other commands that are separated by semicolons can be added to the command line along with the settings. This defines a horiontal script. The script can include commnents that are isolated by semicolons. The horizontal script can be edited and tested repeatedly within PyMOL for many cycles without using an external text editor. This saves time during the development of a new molecular scene. The cursor can be moved around quickly on the command line with the readline commands:
+The Python script roundview.py includes the function `roundview()` that reformats the viewing port settings from seven rows to one row. The more compact format from roundview() is easy to copy and paste onto the command line. Other commands that are separated by semicolons can be added to the command line along with the settings. This defines a horiontal script. The script can include comments that are isolated by semicolons. The horizontal script can be edited and tested within PyMOL for many iterations without using an external text editor. This saves time during the development of a new molecular scene. The cursor can be moved quickly on the command line with the readline commands:
 
 * **cntrl-a**  moves cursor to the beginning of the line
 * **cntrl-e**  moves cursor to the end of the line
@@ -78,12 +78,12 @@ Watch this 1 minute video or read on.
 [![IMAGE ALT TEXT HERE](http://img.youtube.com/vi/watch?v=GnRtEhGvPBQ/0.jpg)](http://www.youtube.com/watch?v=GnRtEhGvPBQ)
 
 
-Copy script from [this link](https://github.com/MooersLab/EasyPyMOL/blob/master/roundview.py) after clicking on "RAW" in the upper right corner and paste into a plain text file (NOT a doc, docx, or rtf file). Name the script [`roundview.py`](./roundview.py). Save the file to your home directory (e.g., /Users/username or /home/username or C:\Users\username). Start PyMOL. Check that PyMOL's current directory is the home directory by entering "pwd" on the command line in PyMOL. Check for presence of roundview.py by entering  "ls *.py" on the command line in PyMOL. 
+Copy script from [this link](https://github.com/MooersLab/EasyPyMOL/blob/master/roundview.py) after clicking on "RAW" in the upper -hand corner and paste into a plain text file (NOT a doc, docx, or rtf file). Name the script file [`roundview.py`](./roundview.py). Save the file to your home directory (e.g., /Users/username or /home/username or C:\Users\username). Start PyMOL. Check that PyMOL's current directory is the home directory by entering "pwd" on the command line in PyMOL. Check for presence of roundview.py by entering  "ls *.py" on the command line in PyMOL. 
 
 ```shell
 ls *.py
 ```
-Paste the following horizontal script on the command line just below the command history window in the top or external gui:
+Paste the following horizontal script on the command line in PyMOL just below the command history window in the top or external gui:
 ```shell
 fetch 1lw9, async=0; run roundview.py; roundview 0,1
 ```
@@ -92,12 +92,12 @@ You should see the following in the command history window of the top gui:
 set_view (1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,-155.2,35.1,11.5,9.7,122.3,188.0,-20.0);
 ```
 
-Type the following to see the default format from get_view.
+Type the following to see the default format from get_view().
 ```shell
 get_view
 ```
 
-Which looks easier to copy from the command history window and paste onto the command line in PyMOL?
+Does the output from roundview() or from getview() look easier to copy from the command history window and paste onto the command line in PyMOL?
 
 #### More advanced ways to install roundview.py
 
@@ -107,12 +107,12 @@ Get the script. Either download the folder from [this link](https://github.com/M
 git clone https://github.com/MooersLab/EasyPyMOL.git
 ```
 
-You need the program [Git](https://git-scm.com/) installed on your computer. Git is available via macports on a mac or otherwise [see these instructions for installing git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git).
+You need the program [Git](https://git-scm.com/) installed on your computer. Git is available via MNacPorts on a mac or otherwise [see these instructions for installing git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git).
 
 
 There are at least four different ways of loading the script into PyMOL:
 
-1. move [`roundview.py`](./roundview.py) to the working directory of pymol. In pymol, type 
+1. move [`roundview.py`](./roundview.py) to the working directory of PyMOL. In PyMOL, type 
 
    ```py
     run roundview.py
@@ -187,7 +187,7 @@ Usage: `roundview [view, decimal places, outname]`
 Quick test with wildtype bacteriophage T4 lysozyme, 3fa0
 --------------------------------------------------------------------------------
 
-Open up pymol. Copy and paste the entire line below onto the command line in the external gui (the on above the GL viewing port). This is an example of a horizontal script. By hitting the up arrow key, you can recall this command for editing on the command line. This code block is more agile to edit than opening, editing, saving, and loading an external script file.
+Open up PyMOL. Copy the entire line below and paste onto the command line in the external gui (the on above the GL viewing port). This is an example of a horizontal script. By hitting the up arrow key, you can recall this command for editing on the command line. This code block is more agile to edit than opening, editing, saving, and loading an external script file.
 
 ```py
 fetch 3fa0,async=0;orient;turn z,-90;turn y,-5;turn x,10; hide everything; bg_color white; show cartoon;color red, ss H;color yellow, ss S;color green, ss L+'';roundview  
@@ -209,13 +209,13 @@ To test some other argument values, copy and paste the following command into Py
 PyMOL>roundview 0,1,firstscene.txt
 ```
 
-Do a `ls *.txt` to list the files in the working diretory. The file "firstscene.txt" should be listed. The default filename is "roundedview.txt". This file is appended with each execution of the roundview command. You may find it easier to copy the set_view line from this text file than from the command history window in PyMOL.
+Enter `ls *.txt` to list the files in the working diretory. The file "firstscene.txt" should be listed. The default filename is "roundedview.txt". The output from roundivew is added to the bottom of this file after each execution of the roundview command. Sometimes, you may find it easier to copy the set_view line from this text file than from the command history window in PyMOL.
 
-## Scripts that use aliases to horizontal scripts. Some aliases contain compact scene settings from roundview().
+## Scripts that use aliases to horizontal scripts. 
 
 ### Exam2function.py
 
-  Defines aliases q1-q8 for questions 1-8 from exam 2 of the OUHSC Macromolecular Systems course. Each alias is 
+  Defines the aliases q1-q8 for questions 1-8 from exam 2 of the OUHSC Macromolecular Systems course. Each alias is 
   is mapped to a number of commands.  
   
   Create ~/Scripts/PyMOLScripts and store the script in this subfolder. 
@@ -228,15 +228,15 @@ run ~/Scripts/PyMOLScripts/exam2function.py
 
 Now the aliases q1,q2, ..., q8 are active.
   
-Type 'q1' to execute the alias assoicated with exam quesitno 1.
+Type 'q1' to execute the alias assoicated with exam quesition 1.
   
 Type 'help q1' to print the documentation to the PyMOL command history window. 
 The bottom of the documentation includes the corresponding horizontal script.
 All or parts of the horizontal script can be copied from the command history 
 window for reuse of the code in another horizontal script or a traditional 
 vertical script.
   
-Tested on PyMOL versions 1.5.0.5, 1.7.7.2 (from macports), and 1.8.0.5. 
+Tested on PyMOL versions 1.5.0.5, 1.7.7.2 (from MacPorts), and 1.8.0.5. 
 
 
 ### StartupAliases.py
@@ -250,11 +250,11 @@ run ~/Scripts/PyMOLScripts/StartUpAliases.py
 ```
 Now these aliases will be available whenever you startup PyMOL.
 
-Type the 'alias name' to execute it.
+Type the 'alias <name>' to execute it.
 
-Type 'help alias name' to see the documentation, which includes a vertical list of the commands mapped to the alias to ease the copying of isolated commands from the command history window during code reuse. The corresponding horizontal script without line breaks is also printed. It can be selected in the command history window and pasted onto the command line. 
+Type 'help alias <name>' to see the documentation, which includes a vertical list of the commands mapped to the alias to ease the copying of isolated commands from the command history window during code reuse. The corresponding horizontal script without line breaks is also printed. It can be selected in the command history window and pasted onto the command line. 
 
-Format of list below:
+Format for the list of aliases below:
 
 Alias name, description: PDB code, where applicable. 
   
@@ -282,9 +282,9 @@ Alias name, description: PDB code, where applicable.
 * **CB**, Define color blind compatible coloring scheme. 
 * **BW**, Make black and white ribbon cartoon on white background.
 * **CSS**, Color ribbon and cartoons by secondary structure: red, green and yellow. 
-* **CBSS**, Color ribbon and cartoons with dcolorblind friendly colors. 
-* **CR**, Commands to make colored filled-ring cartoon of nucleic acids..
-* **FR**, Commands to make filled-ring cartoon of nucleic acids.
+* **CBSS**, Color ribbon and cartoons with colorblind-friendly colors. 
+* **CR**, Commands to make colored filled-ring cartoons of nucleic acids.
+* **FR**, Commands to make filled-ring cartoons of nucleic acids.
 
 #### Demo 1: 
 
@@ -299,18 +299,18 @@ PyMOL>help AO
  
 DESCRIPTION
     
-    Commands to make ambient occlusion image like those in Qutemole. 
+    Commands to make ambient occlusion image like those from the program Qutemole. 
     
     
 USAGE
     
     Type 'AO' to activate. Type 'help AO' to see this documentation
     printed to the command history window. Select from the command
-    history individual lines of code to build a new script. Select the
+    history window the individual lines of code to build a new script. Select the
     hortizontal script at the bottom if retaining most of the commands
     in your new script. Copy and paste onto the comand line below.
     Works only with the command line immediately under the command
-    history window at the top of the gui.
+    history window at the top of the PyMOL gui.
     
     set_color oxygen, [1.0,0.4,0.4];
     set_color nitrogen, [0.5,0.5,1.0];
@@ -349,7 +349,7 @@ Type "U8" on the command line. Convert this to black and white with "BW".
 
 #### Demo 4: 
 
-Type 'help NA' to see a very long script mapped to two a letter command.
+Type 'help NA' to see a very long script mapped to a two-letter command.
 
     DESCRIPTION
 
@@ -438,7 +438,7 @@ Type 'help NA' to see a very long script mapped to two a letter command.
     delete all;viewport 900,600;fetch 3nd4, type=pdb,async=0;run ~/Scripts/PyMOLScripts/quat.py;quat 3nd4; show sticks;set stick_radius=0.125;hide everything, name H*;bg_color white;create coorCov, (3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)));bond (coorCov//A/NA`19/NA),(coorCov//A/A`3/N7); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`119/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`219/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`319/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`419/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`519/O);distance (3nd4_1 and chain Aand resi 19 and name NA), (3nd4_1 and chain A and resi 519);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 419);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 119);distance (3nd4_1 and chain A and resi 19 and name NA),(3nd4_1 and chain A and resi 319);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 219);show nb_spheres; set nb_spheres_size, .35;distance hbond1,/3nd4_1/1/A/HOH`119/O, /3nd4_1/1/A/A`3/OP2;distance hbond2,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/A`3/OP2;distance hbond3,/3nd4_1/1/A/HOH`91/O, /3nd4_1/1/A/HOH`119/O;distance hbond4,/3nd4_1/1/A/G`4/N7,/3nd4_1/1/A/HOH`91/O;distance hbond5,/3nd4_1/1/A/G`4/O6, /3nd4_1/1/A/HOH`419/O;distance hbond6,/3nd4_1/1/A/HOH`91/O, /3nd4_1/1/A/G`4/OP2;distance hbond7,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/G`2/OP2;distance  hbond9,/3nd4_1/1/A/HOH`419/O,/3nd4_2/2/A/HOH`74/O;distance hbond10,/3nd4_2/2/A/C`15/O2,/3nd4_1/1/A/G`2/N2;distance hbond11, /3nd4_2/2/A/C`15/N3,/3nd4_1/1/A/G`2/N1;distance hbond12,/3nd4_2/2/A/C`15/N4,/3nd4_1/1/A/G`2/O6;distance hbond13, /3nd4_2/2/A/U`14/N3,/3nd4_1/1/A/A`3/N1;distance hbond14,3nd4_2/2/A/U`14/O4,/3nd4_1/1/A/A`3/N6;distance hbond15, /3nd4_2/2/A/C`13/N4,/3nd4_1/1/A/G`4/O6;distance hbond16,/3nd4_2/2/A/C`13/N3, /3nd4_1/1/A/G`4/N1;distance hbond17, /3nd4_1/1/A/G`4/N2,/3nd4_2/2/A/C`13/O2;distance hbond18,/3nd4_1/1/A/G`2/N2,/3nd4_2/2/A/C`15/O2;distance hbond19,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2;set depth_cue=0;set ray_trace_fog=0;set dash_color, black;set label_font_id, 5;set label_size, 36;set label_position, (0.5, 1.0, 2.0);set label_color, black;set dash_gap, 0.2;set dash_width, 2.0;set dash_length, 0.2;set label_color, black;set dash_gap, 0.2;set dash_width, 2.0;set dash_length, 0.2;select carbon, element C; color yellow, carbon;disable carbon;set_view (-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0); 
 
 
-Type "NA" to get the resulting image of a sodium cation bound with inner sphere coordination to the N7 nitrogen of an adenine and to five waters. The sodium is in the major groove of a double-strande RNA molecule (PDB-ID 3nd4). The dashed lines represent hydrogen bonds. The numbers are distances in angstroms.
+Type "NA" to get the image of a sodium cation bound with inner sphere coordination to the N7 nitrogen of an adenine and to five waters. The sodium is in the major groove of a double-stranded RNA molecule (PDB-ID 3nd4). The dashed lines represent hydrogen bonds. The numbers are distances in angstroms.
 
 ![naadenine](https://cloud.githubusercontent.com/assets/15176203/13609887/853536a4-e520-11e5-9978-9ea1da4f0884.png)
 
