atom_comp Brian Sykes Lab

Reference

Software Release Notes

Installation

1. First, before downloading the software, make sure you have "wish" in your path. Type 'which wish' in a terminal window and it should come back with a location (eg, /usr/bin/wish). If you don't have it, you may need to install tcl/tk on your machine first.

2. Next, download the software from www.bionmr.ualberta.ca/download/atom_comp

3. untar it

   		> tar xvf atom_comp*.tar
   

4. Copy the atom_comp script to a public place or your $HOME/bin directory.

   		> cd atom_comp/src/bin 
   		> cp atom_comp /usr/local/bin
   

Example

1. Make sure you have an ensemble pdb file. In this example we have 30 models. Use spaces or tabs to delimit the fields. Each line contains one atom pair for comparison.

2. Place protein atoms in a file

   # Protein  atoms
   LYS 90  A   NZ  1.602E-19
   LYS 92  A   NZ  1.602E-19
   ARG 102 A   CZ  1.602E-19
   LYS 106 A   NZ  1.602E-19
   LYS 118 A   NZ  1.602E-19
   LYS 138 A   NZ  1.602E-19
   LYS 142 A   NZ  1.602E-19
   ARG 147 A   CZ  1.602E-19
   LYS 158 A   NZ  1.602E-19
   GLU 94  A   CD  -1.602E-19
   GLU 95  A   CD  -1.602E-19
   GLU 96  A   CD  -1.602E-19
   ASP 99  A   CG  -1.602E-19
   ...
   

3. Place peptide atoms in a file

   # Peptide File
   LYS 139 B   NZ    0
   ARG 140 B   CZ    0
   THR 142 B   OG1   0
   ARG 144 B   CZ    0
   ARG 145 B   CZ    0
   ARG 140 B   CZ    0
   ARG 147 B   CZ    0
   LYS 137 B   NZ    0
   ASP 133 B   CG    0
   

4. Within a terminal window type "atom_comp". You should get the following atom_comp gui. Next, enter your 3 input files and an output file.

   

5. Click the "Read Data" button.

   

6. Select the atoms to use in energy calculations. Click the "Calculate" button.

   

7. The output will look similar to this.

   

Back to main software page

This file last updated: