exam2.py

from __future__ import print_function
# -*- coding: utf-8 -*-
"""
    DESCRIPTION AND INSTALLATION

        Defines aliases for exam 2 of the OUHSC Macromolecular Systems course.
        The aliases have actually been recoded as python functions but they
        can be thought of as aliases.
         
        Create ~/Scripts/PyMOLScripts
        and store the script in this subfolder 
        or store in some other folder of your choosing IF you know what you are doing. 
        
        Enter on the command line in PyMOL the following command:
        
        run ~/Scripts/PyMOLScripts/S4_File.py
        
        Now the aliases q1,q2, ..., q8 are active.
        
        Tested on PyMOL versions 1.5.0.5, 1.8.0.5, 1.8.2.0. 
                
    Copyright Notice
    ================
    Copyright (C) 2016  Blaine Mooers

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
    See the GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

    The source code in this file is copyrighted, but you can
    freely use and copy it as long as you don't change or remove any of
    the copyright notices.

    Blaine Mooers , PhD 
    blaine-mooers@ouhsc.edu
    975 NE 10th St, BRC 466
    University of Oklahoma Health Sciences Center
    Oklahoma City, OK, USA 73104
""" 
from pymol import cmd
__author__ = "Blaine Mooers"
__copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104"
__license__ = "GPL-3"
__version__ = "1.0.3"
__credits__ = ["William Beasley","Chiedza Kanyumbu"] 
# people who reported bug fixes, made suggestions, etc. 
__date__ = "24 July 2016"
__maintainer__ = "Blaine Mooers"
__email__ = "blaine-mooers@ouhsc.edu"
__status__ = "Production" 

print("2015 OUHSC MSI-Lecture 17 and 18 takehome exam")
print("on nucleic acid structure.")
print(" ")
print("Enter 'q1' for question 1, 'q2' for question 2, ...,")
print("'q8' for question 8.")
print(" ")
print("Questions (1-4). HIV reverse transcriptase bound to DNA")
print("with AZT incorporated (PDB-ID 3V6D).")
print(" ")
print("Questions (5-8). The full-length hammerhead")
print("ribozyme (PDB-ID 3zp8).")
print(" ")
print("Enter 'help exam2' to learn how to use this script.")
print("Enter 'help q1' to see quesiton 1 and the corresponding horizontal script.")
print(" ")
print("All or part of the horizontal script can be copied from the command history window for reuse.")
print(" ")
print("Positon cursor on command line with left mouse button.")
print("Readline commands move the cursor to left or right:")
print("     control-a will move the cursor to the beginning of the command line.")
print("     control-e will move the cursor to the end of the line.")
print("     command-f will move the cursor to the end of the current word.")
print("     command-b will move the cursor to the begining of the current word.")
print("     control-f will move the cursor to the right one character.")
print("     control-b will move the cursor to the left by one character.")
print(" ")
print("Enter 'help rline' to see these commands again in the command history window.")
print(" ")
print("Up arrow key recalls last line of commands for editing.")



def exam2():
    """
    USAGE:
    
        Enter 'run exam2.py' without including the quotation marks. 
        
        Enter 'q1' to make the molecular scene for question 1. 
        (Need active internet connection). 
        
        Enter 'help q1' to see question 1 and the commands used to 
        make the molecular scene. 
        
        When you are ready for question 2, 
        enter 'q2' for question 2, and so on. 
        
        Enter 'help rline' to see the commands to move cursor on command line.

    DESCRIPTION

        Defines the molecular scenes for MSI-Lecture 17 and
        18 takehome exam.    
        
        Each question with a molecular scene has the scene
        defined by a specific function qX(), where X is the
        number of the question. 
        
        Each function defines a series of PyMOL commands. Each
        function also has its own documentation that explains
        the molecular scene and that is printed to the
        command history window when you type 'help q1' or
        'help q2' and so on. 
        
        Each row of commands starts with 'reinitialize' to 
        remove old molecules and settings. Each
        function prints to the command history window
        an alias to the commands in the function. 
        
    LIMITATIONS
        
        An active internet connection is required because 
        each alias uses the fetch command. 
        
        Replace the fetch command with the load command to 
        load atomic coordinates from your harddrive. 
        
        Enter "rock" to stop the rocking motion.
        
    REQUIREMENTS
            
        When developing a variant of this program., run the 
        program roundview.py to obtained a shorter version 
        of the viewport settings.

    NOTES
    
        Use gray scroll bar to the right side of the command 
        history window to see all of this documentation. or hit 
        escape after moving the cursor to the viewing port 
        (the GUI with the molecule). 

  Copyright Notice
  ================
  
  The PyMOL function source code in this file is copyrighted, but you can
  freely use and copy it as long as you don't change or remove any of
  the copyright notices.
  
    """ 
    print("The function exam2() stores this docstring.")
cmd.extend( "exam2",exam2)


def rline():
       '''
    DESCRIPTION
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.
        '''
cmd.extend("rline",rline)


def q1():
    '''
    DESCRIPTION

    Question 1: Explain how AZT terminates extension of the DNA chain. 
    
    The following commands created the scene for "q1": 
    
    delete all; fetch 3v6d, HIVrt, async=0; rock;preset.ball_and_stick("c. P and i. 822");set_view (-0.99,-0.1,0.06,0.09,-0.39,0.92,-0.07,0.92,0.39,0.0,0.0,-29.2,-10.56,24.72,39.27,23.02,35.38,-20.0); 

    To reuse of parts or all of the above commands, copy and paste the commands 
    onto the command line or into a plain text file. 
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.
    '''
    cmd.reinitialize()
    cmd.fetch('3v6d', type='pdb', name='HIVrt',async='0')
    cmd.rock()
    preset.ball_and_stick('c. P and i. 822')
    cmd.set_view('(-0.99,-0.1,0.06,0.09,-0.39,0.92,-0.07,\
    0.92,0.39,0.0,0.0,-29.2,-10.56,24.72,39.27,\
    23.02,35.38,-20.0)') 
    print('Enter "q1" to set scene for question 1.')
    print('Enter "help q1" for more information.') 
cmd.extend( 'q1',q1)



def q2():
    '''
    DESCRIPTION

    Question 2: Look along the helical axis of the DNA. 
    Is the DNA helix bent?
    
    The following commands created the scene for "q2": 

    delete all; fetch 3v6d, HIVrt, async=0; rock;show cartoon, c. P or c. T;set_view (0.61,0.29,-0.73,0.78,-0.37,0.51,-0.12,-0.88,-0.45,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);  
    
    To reuse of parts or all of the above commands, copy and paste the commands 
    onto the command line or into a plain text file. 
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.

    '''
    cmd.reinitialize()
    cmd.fetch('3v6d',type='pdb',name='HIVrt',async='0')
    cmd.rock()
    cmd.show_as("cartoon","chain P or chain T")
    cmd.set_view('(0.61,0.29,-0.73,0.78,-0.37,0.51,-0.12,-0.88,-0.45,-0.0, 0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);')
    print('Enter "q2" to make the scene for question 2.')    
    print('Enter "help q2" to see question 2 and the commands to make the scene.')
cmd.extend( 'q2',q2)


def q3():
    '''
    DESCRIPTION

    Question 3: In which groove of the DNA 
    is the protein making the most contacts? 
    Is this unusual? 
    
    The following commands created the scene for "q3": 
    
    delete all; fetch 3v6d, HIVrt, async=0; show cartoon, c. A or c. B;hide lines, c. A or c. B;set_view (0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);rock;

    To reuse of parts or all of the above commands, copy and paste the commands 
    onto the command line or into a plain text file. 
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.
    '''
    cmd.reinitialize()
    cmd.fetch('3v6d', type='pdb', name= 'HIVrt', async='0')
    cmd.show_as("cartoon","c. A or c. B") 
    cmd.hide("lines","c. A or c. B") 
    cmd.rock()
    cmd.set_view('(0.53,-0.06,-0.84,0.82,-0.21,0.53,-0.21,-0.98,-0.07,-0.0,-0.0,-192.99,-29.84,8.42,47.76,178.27,207.7,-20.0);')
    print('Enter "q3" to make the scene for question 3.')
    print('Enter "help q3" to see question 3 and the commands to make the scene.') 
cmd.extend( 'q3',q3)   



def q4():
    '''
    DESCRIPTION

    Question 4:  What the dihedral angle about the disulfide
    bond between MRG81 of chain F and Cys258 of chain C?
    This is a cross link between the protein and the DNA. Is
    this a cis or trans conformation of the bonds about the
    S--S bond? Is this conformation energetically favorable
    or unfavorable? 
    
    The following commands created the scene for "q4": 
 
    delete all; fetch 3v6d, HIVrt, async=0;preset.ball_and_stick("(c. C and i. 258) or (c. F and i. 817 )");set_view (0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0); 

    To reuse of parts or all of the above commands, copy and paste the commands 
    onto the command line or into a plain text file. 
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.
    '''
    cmd.reinitialize()
    cmd.fetch('3v6d',type='pdb',name='HIVrt',async='0')
    cmd.do("preset.ball_and_stick(selection='(chain C and resi 258) or (chain F and resi 817 )')")
    cmd.set_view('(0.21,-0.91,0.34,-0.84,0.01,0.54,-0.5,-0.4,-0.77,0.0,-0.0,-38.82,-39.67,-55.1,10.96,36.31,41.34,-20.0);')
    cmd.rock()
    print('Enter "q4" to make the scene for question 4.')
    print('Enter "help q4" to see question 4 and the commands to make the scene.') 
cmd.extend('q4',q4)



def q5():
    '''
    DESCRIPTION

    Question 5:  How many axial stacks of helices does 
    the ribozyme have?
    
    The following commands created the scene for "q5": 
    
    delete all;fetch 3zp8, hammer, async=0;show cartoon, hammer;set_view (-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);rock;

    To reuse of parts or all of the above commands, copy and paste the commands 
    onto the command line or into a plain text file. 
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.
    '''
    cmd.reinitialize()
    cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
    cmd.show_as('cartoon','hammer')
    cmd.rock()
    cmd.set_view('(-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);')
    print('Enter "q5" to make the scene for question 5.')
    print('Enter "help q5" to see question 5 and the commands to make the scene.') 
cmd.extend('q5',q5)


def q6():
    '''
    DESCRIPTION

    Question 6:  What is the average distance of the Na1044
    ligand bonds? Give the residue numbers of the RNA
    nucleotides and the sodium to identify them. How many
    ligands are from RNA?
   
    The following commands created the scene for "q6":
     
    delete all;fetch 3zp8, hammer, async=0; rock;preset.ball_and_stick("all");distance ligand1, i. 1044, c. A and i. 22 and n. N7;distance ligand2, i. 1044, c. A and i. 21 and n. OP2;distance ligand3, i. 1044, i. 2121;distance ligand4, i. 1044, i. 2120;distance ligand5, i. 1044, i. 2122;distance ligand6, i. 1044, i. 2130;set_view (-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0);

    To reuse of parts or all of the above commands, copy and paste the commands 
    onto the command line or into a plain text file. 
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.
    '''
    cmd.reinitialize()
    cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
    cmd.rock()
    cmd.do('preset.ball_and_stick("all")')
    cmd.distance('Sodiumligand1',' resi 1044', 'chain A and i. 22 and n. N7')
    cmd.distance('Sodiumligand2', 'resi 1044', 'chain A and i. 21 and n. OP2')
    cmd.distance('Sodiumligand3', 'resi 1044', 'resi 2121')
    cmd.distance('Sodiumligand4', 'resi 1044', 'resi 2120')
    cmd.distance('Sodiumligand5', 'resi 1044', 'resi 2122')
    cmd.distance('Sodiumligand6', 'resi 1044', 'resi 2130')
    cmd.do('set label_size, -0.4')
    cmd.set_view('(-0.87,0.18,-0.46,-0.39,-0.81,0.44,-0.29,0.56,0.78,-0.0,0.0,-20.47,-18.05,14.02,-18.89,17.47,23.47,-20.0);')   
    print('Enter "q6" to make the scene for question 6.')
    print('Enter "help q6" to see question 6 and the commands to make the scene.') 
cmd.extend('q6',q6)


def q7():
    '''
    DESCRIPTION

    Question 7:  Measure the longest dimension and the
    shortest dimension of the ribozyme. Enter "rock" to 
    stop the rocking motion. What is the ratio of
    the longest dimension to the shortest dimension? Is it
    globular like a protein?  
    
    The following commands created the scene for "q7": 

    delete all;fetch 3zp8, hammer, async=0;show ribbon, hammer;set_view (0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0); rock;

    To reuse of parts or all of the above commands, copy and paste the commands 
    onto the command line or into a plain text file. 
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.
    '''
    cmd.reinitialize()
    cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
    cmd.show_as('ribbon', 'hammer')
    cmd.rock()
    cmd.set_view('(0.62,0.14,0.78,0.13,-0.99,0.07,0.78,0.05,-0.63,-0.0,-0.0,-169.8,-16.43,9.44,-9.63,143.54,196.05,-20.0);')
    print('Enter "q7" to make the scene for question 7.')
    print('Enter "help q7" to see question 7 and the commands to make the scene.') 
cmd.extend('q7',q7)


def q8():
    '''
    DESCRIPTION

    Question 8:  Find the unusual base pair between A21 and
    G36. What is the length of the H-bonds between the bases
    (ignore the H atoms in the distance measurement)? List
    the distance with the residue name, residue number, and
    atom name. What additional H-bond occurs between a base
    in this base pair and a ribose ring of one of the two
    nucleotides in this base pair? 
   
    The following commands created the scene for "q8": 
    
    fetch 3zp8, hammer, async=0;hide everything;show ribbon;show sticks, resi 21 or resi 36;set_view (-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);rock; 

    To reuse of parts or all of the above commands, copy and paste the commands 
    onto the command line or into a plain text file. 
      
    These commands are sufficient for most editing tasks:  
    To edit code, positon cursor on command line with left mouse button.  
    Control-e moves the cursor to the end of the line, even when it is out of view.
    Control-a moves the cursor to the beginning of the line, even when it is out of view.    
    Up arrow key recalls last line of commands for editing.

    These commands may not be available on all systems:
    Shift-control-a selects everything from the right of the cursor to the end of the line.
    Shift-control-e selects everything to the left of the cursor to the end of the line.
    Command-f moves the cursor to the end of the current word.   
    Command-b moves the cursor to the begining of the current word.
    Control-f moves the cursor to the right by one character.   
    Control-b moves the cursor to the left by one character.
    '''
    cmd.reinitialize()
    cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
    cmd.show_as('ribbon', 'hammer')
    cmd.rock()
    cmd.hide('everything')
    cmd.show_as( 'ribbon','all') 
    cmd.show_as('sticks', 'resi 21 or resi 36')
    cmd.set_view('(-0.9,-0.19,0.39,0.39,-0.74,0.55,0.19,0.65,0.74,0.0,0.0,-37.58,-21.66,15.71,-23.32,35.42,39.74,-20.0);')
    print('Enter "q8" to make the scene for question 8.')
    print('Enter "help q8" to see question 8 and the commands to make the scene.') 
cmd.extend('q8',q8)