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EBI Groups Thornton Software NUCPLOT Installation Instructions

NUCPLOT Installation Instructions

1. Download NUCPLOT

You can obtain the latest version of the NUCPLOT programs here:
 
NUCPLOT programs
 
Click on the icon on the left to download either the nucplot.zip file, which contains the NUCPLOT source code, or winnucplot.zip, which contains the executable program for Windows.

 

2. Install the programs

a. Linux and mac

  1. After downloading the nucplot.zip file, move it to an appropriate location. Then unzip as follows:
    unzip nucplot.zip
    This will create two directories called nucplot and hbplus containing the source code for NUCPLOT and HBPLUS, respectively.

  2. Go into the hbplus directory and compile the HBPLUS programs by typing:
    make
    If this doesn't work, compile using the following two commands:
    gcc -c *.c
    gcc -o hbplus hbp_gen.o hbp_inpdb.o hbp_findh.o hbp_hhb.o hbp_qnh.o hbp_main.o -lm
    Either way, you should get an executable file called hbplus.

  3. Now go into the nucplot directory and compile the NUCPLOT programs by typing:
    gcc -o nucplot nucplot.c -lm
    gcc -o hbadd hbadd.c -lm
    -lm is an option that includes the Standard Maths library.
     
    You should get two executable files called nucplot and hbadd.

b. Windows

After downloading the winnucplot.zip file, right-click on it and select Extract All.
 
When prompted, choose to extract to C:\, or wherever else you would like to store the programs. A directory called nucplot will be created containing the executable file, nucplot.exe.

 

3. Download the Het Group Dictionary

The HBADD program uses the information in the PDB's Het Group Dictionary to help HBPLUS determine which atoms in a ligand are potential hydrogen bond donor and acceptors. For HBADD to run, you need to download a copy of the Het Group Dictionary using the following command from the nucplot executable directory:
wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif

Windows

For Windows, the above command needs to be executed using the "Command Prompt" window. You can open this window by typing "command" into the Windows search box at the bottom left of your screen:
 


 
Then, click on the "Command Prompt" app:

 


 
And you will get the Command Prompt window:
 


 
You can now change to the nucplot directory and run the wget command as above. eg
cd C:\nucplot
wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif

 

4. Assignment of aliases/logical names

To make it easy to run the NUCPLOT program you need to create aliases for the program directories and program names, as described below.

a. Linux and mac

Add the following aliases to your .bashrc/.cshrc/.zshrc, etc file according to which shell you are running (ie the bash shell or some other, like C-shell or Z-shell)
 
.cshrc/.zshrc files
 
Add
# NUCPLOT
# -------
set nucdir = 'nucplot-directory'
setenv nucdir 'nucplot-directory'
set hetdic = $nucdir'/components.cif'
alias nucplot $nucdir'/nucplot.scr'
alias nuconly $nucdir'/nuconly.scr'
 
# HBPLUS
# ------
set hbdir = 'hbplus-directory'
setenv hbdir 'hbplus-directory'
alias hbplus $hbdir'/hbplus'
where 'nucplot-directory' and 'hbplus-directory' are the directory locations of the NUCPLOT and HBPLUS executables.
 
.bashrc file
 
Add
# NUCPLOT
# -------
export nucdir='nucplot-directory'
alias hetdic=$nucdir'/components.cif'
alias nucplot=$nucdir'/nucplot.scr'
alias nuconly=$nucdir'/nuconly.scr'
 
# HBPLUS
# ------
export hbdir='hbplus-directory'
alias hbplus=$hbdir'/hbplus'
where 'nucplot-directory' and 'hbplus-directory' are the locations of the NUCPLOT and HBPLUS executables.
 
You can activate the new aliases by typing:
source .cshrc
or
source .bashrc
You can now run the program by typing nucplot, followed by the name of the PDB file to be analysed. For further information, see the Operating Manual.

b. Windows

Open a "Command Prompt" window, as described above.
 
You can check whether the installed executables are compatible with your version of Windows. Go to the nucplot directory using the cd command. For example, if you installed the programs in C:\, the commands would be:
> cd C:\nucplot\exe
If you installed the program elsewhere, then the path in the command will need to be changed accordingly. For example, if you uzipped it into C:\Users\yourname, it becomes:
> cd C:\Users\yourname\nucplot\exe
Then type:
> .\nucplot
If all is OK, you will see the following message: 

Reading parameter file ...

USAGE:
      nucplot PDB_file

   where:-   PDB_file = name of input PDB file
If not, you will see something like: 

.\nucplot: Exec format error. Binary file not executable.
or 

'.\nucplot' is not recognized as an internal or external command, operable program or batch file.

 
In which case, please contact roman@ebi.ac.uk.
 
For convenience, it is a good idea to add the name of the nucplot directory to your system path. You can do this using the following command:
set PATH=%PATH%;"C:\nucplot"
replacing C:\nucplot with the correct directory, if different.
 
To save having to issue this command each time you open a new Command Prompt window, you can permanently add the nucplot directory to your path as described here, or here.
 
Once the path has been set you can run NUCPLOT by typing nucplot from any directory.

 

4. Running NUCPLOT

Instructions for running the program can be found in:
NUCPLOT Manual