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--- building_a_hydrate_lattice [2018/05/08 11:34] – edit
+++ building_a_hydrate_lattice [2018/05/08 11:48] (current) – edit
@@ Line 7: / Line 7: @@
 **__Getting Oxygen Atom Coordinates__**
-- Go to http://www.crystallography.net/cod/
+- Go to http://www.crystallography.net/cod/ \\
-- Click on Search under Accessing COD Data on the left side
+- Click on Search under Accessing COD Data on the left side  \\
-- Search by DOI: 10.1021/ja049247c
+- Search by DOI: 10.1021/ja049247c  \\
     Paper associated with above DOI:
@@ Line 15: / Line 15: @@
     Michael T. Kirchner, Roland Boese, W. Edward Billups, and Lewis R. Norman
-  - For structure I, use COD ID: 4112809
+ - For structure I, use COD ID: 4112809  \\
-  - For structure II, use COD ID: 4112807
+ - For structure II, use COD ID: 4112807  \\
 - Click on "CIF" under next to the COD ID to download the .cif file
     (see 4112809.cif and 4112807.cif)
-You can use the software Avagadro to open the .cif file
+ - You can use the software Avagadro to open the .cif file  \\
-You can download Avagadro from here: https://avogadro.en.softonic.com/
+ - You can download Avagadro from here: https://avogadro.en.softonic.com/  \\
-- Open the .cif file with Avagadro
+- Open the .cif file with Avagadro  \\
-- You will see a unit cell for the structure
+- You will see a unit cell for the structure \\
-- Click on Build->Cartesian Editor
+- Click on Build->Cartesian Editor \\
-Sort by Element
+- Sort by Element \\
-Delete all the non-oxygen atoms and their coordinates
+- Delete all the non-oxygen atoms and their coordinates \\
-(delete all lines that do not start with the letter O)
+ - (delete all lines that do not start with the letter O) \\
-click apply and exit out of the Cartesian Editor
+- Click apply and exit out of the Cartesian Editor \\
-You should see a less crowded unit cell with only the Oxygen atoms
+ - You should see a less crowded unit cell with only the Oxygen atoms \\
-Now we will save the coordinates as a .pdb file
+ - Now we will save the coordinates as a .pdb file  \\
-click on "File->Save as", select PDB under "Save as type" and save the file
+- Click on "File->Save as", select PDB under "Save as type" and save the file \\
-(see 4112809_justOxygen.cif and 4112807_justOxygen.cif)
+    (see 4112809_justOxygen.cif and 4112807_justOxygen.cif)
-Using Avicci
+**__Using Avicci__**
-You will need to have Java installed to use this program.
+You will need to have Java installed to use this program.  \\
-Click on Avicci.jar to launch the program
+Click on Avicci.jar to launch the program \\
-Specify the inputs:
-- Input path: Enter the absolute path for the .pdb file that contains the coordinates of the oxygen atoms
-- Output path: Enter the absolute path for the .pdb file that will contain the final slab (include the name of the output file in the path)
-- Structure: Enter 1 for structure I or 2 for structure II
-- Fraction Methane in Small Cages: Enter a value between 0 and 1 inclusive (All cages in structure I are considered small cages)
-- Fraction Methane in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I)
-- Fraction Cyclohexane in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I)
-- Fraction Benzene in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I)
-- Water Model ( 1 for TIP4P-EW , 2 for TIP4P-2005 ): Enter 1 or 2
-- Slab Size A: Size of final slab in the X direction as a multiple of the unit cell size, Enter a value greater than zero
-- Slab Size B: Size of final slab in the Y direction as a multiple of the unit cell size, Enter a value greater than zero
-- Slab Size C: Size of final slab in the Z direction as a multiple of the unit cell size, Enter a value greater than zero
-Example: A = 2 , B = 2 , C = 1 creates a 2 X 2 X 1 slab of the unit cell in the input file
-- Number of spaces to 1st coordinate: Number of words/spaces before the x-coordinate in the input .pdb file, used for parsing the coordinates (Enter 5 as the default value)
-Click "Generate Hydrate" to execute the program and close the program. Check the ouptput path for the results of the program.
+__Specify the inputs:__ \\
+- __Input path:__ Enter the absolute path for the .pdb file that contains the coordinates of the oxygen atoms  \\
-(see 4112809_justOxygen_output.cif and 4112807_justOxygen_output.cif)
+- __Output path:__ Enter the absolute path for the .pdb file that will contain the final slab (include the name of the output file in the path)  \\
+- __Structure:__ Enter 1 for structure I or 2 for structure II  \\
+- __Fraction Methane in Small Cages:__ Enter a value between 0 and 1 inclusive (All cages in structure I are considered small cages)  \\
+- __Fraction Methane in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I)  \\
+- __Fraction Cyclohexane in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I)  \\
+- __Fraction Benzene in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I)  \\
+- __Water Model ( 1 for TIP4P-EW , 2 for TIP4P-2005 ):__ Enter 1 or 2  \\
+- __Slab Size A:__ Size of final slab in the X direction as a multiple of the unit cell size, Enter a value greater than zero  \\
+- __Slab Size B:__ Size of final slab in the Y direction as a multiple of the unit cell size, Enter a value greater than zero  \\
+- __Slab Size C:__ Size of final slab in the Z direction as a multiple of the unit cell size, Enter a value greater than zero  \\
+Example: A = 2 , B = 2 , C = 1 creates a 2x2x1 slab of the unit cell in the input file \\
+- __Number of spaces to 1st coordinate:__ Number of words/spaces before the x-coordinate in the input .pdb file, used for parsing the coordinates (Enter 5 as the default value)   \\
+Click "Generate Hydrate" to execute the program and close the program. Check the ouptput path for the results of the program.  \\
+\\
+\\
+If you have any question, feel free to email me at kmanayer(at)yahoo(dot)com  \\