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EBI Groups Thornton Software PDBsum1 Installation Instructions

PDBsum1 Installation Instructions

PDBsum1

1. Download PDBsum1

You can obtain the latest version of the PDBsum1 programs here:
 
PDBsum1 programs
 
Click on the icon on the left to download the pdbsum1.zip file which contains the PDBsum1 executables and associated files.

 

2. Install the programs

Move pdbsum1.zip to an appropriate location. On Windows, for example, this might be the C:\ drive. Then unpack as follows:

a. Linux and mac

Unzip the file as follows:
unzip pdbsum1.zip
This will create a directory called pdbsum1, and various subdirectories beneath, containing all the necessary files.

b. Windows

Right-click on the file's icon and select Extract All. When prompted, choose to extract to C:\, or wherever else you would like to store the programs. A directory called pdbsum1 will be created containing all the necessary files.
 
 

3. Check the executables

It is a good idea to check whether the installed executables are compatible with your operating system. If not, you can recompile the programs from the supplied source code, as described shortly.

a. Linux and mac

To perform the check on linux or mac, open a terminal window and go to the appropriate executables directory:
  • linux
    cd [fullpath]/pdbsum1/exe_linux
  • mac
    cd [fullpath]/pdbsum1/exe_mac
Then type:
./pdbsum1
If all is OK, you will see the following message: 
Usage is:

pdbsum1 {file [pdb_code] | -l dataset.lst} [-nomaxchn]  [-help]

where
     * file           = Name of single PDB file to be processed
     * pdb_code       = Optional 4-character identifier
     * -l dataset.lst = Name of file listing PDB files to be processed
     * -nomaxchn      = Clefts to be generated even if more than 4 chains in structure
     * -relinks       = Make all image links relative
If not, you will see something line: 
./pdbsum1: Exec format error. Binary file not executable.
or 
'.\pdbsum1' is not recognized as an internal or external command, operable program or batch file.

 
In which case, you will need to recompile the programs as described below.

b. Windows

For Windows, you need to open a "Command Prompt" window. This is the window you will use to run PDBsum1. To open it, enter "command" into the Windows search box at the bottom left of the screen:
 


 
Then, click on the "Command Prompt" app:

 


 
And you will get the Command Prompt window:
 


 
You can now enter the required commands into this window.
 
To check whether the installed executables are compatible with your operating system go to the exe_win directory. If you installed the programs in C:\, the commands will be:
C:
cd C:\pdbsum1\exe_win
If you installed the program elsewhere, then the path in the second command will need to be changed accordingly. For example, if you uzipped the programs into C:\Users\yourname, the second command becomes:
cd C:\Users\yourname\pdbsum1\exe_win
Then type::
.\pdbsum1
If all is OK, you will see the following message: 
Usage is:

pdbsum1 {file [pdb_code] | -l dataset.lst} [-nomaxchn]  [-help]

where
     * file           = Name of single PDB file to be processed
     * pdb_code       = Optional 4-character identifier
     * -l dataset.lst = Name of file listing PDB files to be processed
     * -nomaxchn      = Clefts to be generated even if more than 4 chains in structure
If not, you will see something line: 
./pdbsum1: Exec format error. Binary file not executable.
or 
'.\pdbsum1' is not recognized as an internal or external command, operable program or batch file.

 
In which case, you will need to recompile the programs as described in the next section.
 
 

4. Recompiling the programs

If your check in the previous section gives you an error, you can recompile the programs from this same directory by typing:
source ../scripts/compile.linux - for linux
or
source ../scripts/compile.mac - for mac
Note that, if you have conda installed on your mac, it may interfere with the compilation of the programs. If you get error messages of the form: 
  ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/...' for architecture x86_64 collect2: error: ld returned 1 exit status
Try typing
conda deactivate
and then compile again.
 
For Windows, you will need to have a linux-like environment such as cygwin or Msys2 installed with a C and gfortran compiler, or make use of the Visual Studio build tools. The equivalent command from the exe_win directory will then be:
source ../scripts/compile.win
Contact roman@ebi.ac.uk if you have any problems, stating the version of the operating system that you have.
 
 

5. Download required external packages

PDBsum1 requires a number of 3rd-party packages to run. These are listed below and must be installed or the programs will not be able to run properly. If your system does not already have them, a Google search will help you to find where to obtain them. On mac, you can use Homebrew (https://brew.sh) to install them all.
  1. PyMOL - There are a number of versions of this program available. Many are free - or are available for free as educational versions. Any version from v.0.99 upwards is fine.

  2. ImageMagick convert - PDBsum1 contains many images, and the bulk of the image conversion is performed by the convert utility in the ImageMagick package, which is available from:
    https://imagemagick.org/script/download.php
    Note that, if during running PDBsum1 you get an error of the form: 
    convert: attempt to perform an operation not allowed by the security policy
`PS' @ error/constitute.c/IsCoderAuthorized/408.
    you may need to make the change to the ImageMagick policy.xml file, as described in:
    https://stackoverflow.com/questions/52998331/imagemagick-security-policy-pdf-blocking-conversion

  3. wget - This is a tool for downloading files from the web and is used by PDBsum1 to retrieve a protein's UniProt data and Pfam domains, where relevant.

       
    • On linux systems wget is likely already part of your installation. You can check whether you have it by typing:
      which wget
      If this doesn't find the program, use Google to learn how to install it.
       
    • For Windows systems, the following link will tell you how to get wget:
      https://builtvisible.com/download-your-website-with-wget/
      Save the file in your "C:\Program Files" directory in, say, a subdirectory called wget.

     
  4. ps2pdf - This is a utility for converting PostScript files to PDF and comes as part of the Ghostscript package:
    https://www.ghostscript.com/releases/gsdnld.html
    If you are running on Windows, you will need to update your computer's "PATH" variable to include the Ghostscript bin and lib directories. The former might have already been done automatically for you during installation.
     
    To update your "PATH", follow the instructions applying to your version of Windows, as given here:
    https://www.computerhope.com/issues/ch000549.htm
    The paths you need to add will be of the form:
     
    • C:\Program Files\gs\gs9.56.1\bin
       
    • C:\Program Files\gs\gs9.56.1\lib

     
    where the gs9.56.1 is the Ghostscript version and will depend on which version you have installed.
     
    Once the path has been set, you can test it is correct by typing the name of the application file in the bin directory - eg gswin64. If the path is right, you will see a new window open with a "GS>" prompt. Close the window by entering "quit".

 

5. Download optional packages

The following packages are recommended for download.
  1. RasMol - This was one of the first molecular viewers developed and is still probably the simplest to use, with a fairly intuitive set of commands. Many of the analyses in PDBsum1 (eg beta turns, protein-ligand interactions) can only currently be viewed in 3D using RasMol, so it is recommended you install it.
     
  2. LigPlot+ - This is a program for plotting, and then interactively editing, schematic diagrams of protein-ligand interactions. The Ligands tab on a PDBsum1 page includes a LIGPLOT diagram. If you have LigPlot+ installed, you can click on the LigPlot+ icon to load the diagram into this program for modifying, printing, etc.
     
    The program is freely available to academic institutions. Further information can be found at:
    LigPlot+ home page

 

6. Editing the parameter file

Before you can run PDBsum1, you need to tell the program where certain things are located so that it can find them. This is done by editing a simple text file called CATHPARAM, located in the directory:
pdbsum1/params
Only six parameters need to be edited, as shown in green below:
 
linux example     Windows example 
###########################################################################
#
# Paths and directories for PDBsum1
#
###########################################################################

#
#-- Operating system: linux/win/mac
#
OPERATING_SYSTEM      = linux


#
#-- Location of installed PDBsum1 system and subdirectories
#
PDBSUM1_DIR           = /nfs/userapps/pdbsum1

#
#-- Directory where the results are to be written
#
PDBSUM1_RESULTS_DIR   = /nfs/data/pdbsum1

#
#-- Paths to required external software (put NONE if not available)
#
CONVERT_EXE = /usr/bin/convert
PS2PDF      = /usr/bin/ps2pdf
PYMOL_EXE   = /nfs/research1/software/Linux_x86_64/bin/pymol
WGET        = /usr/bin/wget
    
###########################################################################
#
# Paths and directories for PDBsum1
#
###########################################################################

#
#-- Operating system: linux/win/mac
#
OPERATING_SYSTEM      = win


#
#-- Location of installed PDBsum1 system and subdirectories
#
PDBSUM1_DIR           = C:\PDBsum1

#
#-- Directory where the results are to be written
#
PDBSUM1_RESULTS_DIR   = C:\Users\user\data\PDBsum1

#
#-- Paths to required external software (put NONE if not available)
#
CONVERT_EXE = "C:\Program Files\ImageMagick-7.1.0-Q16-HDRI\convert"
PS2PDF      = "C:\Program Files\gs\gs9.56.1\lib\ps2pdf"
PYMOL_EXE   = "C:\Program Files (x86)\PyMOL\PyMOLWin.exe"
WGET        = "C:\Windows\System32\wget"

 
The parameters you need to define are:
 
  • OPERATING_SYSTEM - This should be linux, mac, or win, and tells the programs which set of executables to use.
     
  • PDBSUM1_DIR - This defines the directory where the PDBsum1 programs are installed. The correct directory will contain the following subdirectories: compile, data, docs, etc.
     
  • PDBSUM1_RESULTS_DIR - This tells PDBsum1 the name of the directory where it is to write all its output files. This directory must exist, so make sure you create it before running the program.
     
  • CONVERT_EXE - The full path to the ImageMagick convert image conversion program.
     
  • PS2PDF - The path of the ps2pdf utility that converts PostScript files to PDF.
     
  • PYMOL_EXE - The path to the PyMOL executable.
     
  • WGET - The path of wget, which downloads files from the web.

 

7. Script for RasMol

Many of the PDBsum1 analyses can be viewed in 3D using the RasMol molecular viewer. These include the structure as a whole, protein-ligand interasctions, and individual ProMotif motifs.
 
PDBsum1 generates RasMol scripts to display these correctly. However, to view them needs a little set-up. There are two scripts in the pdbsum1/scripts directory to help you. Both are called rasscriptstart. The one with the .scr extension is for use on linux or mac, while the .bat one is for Windows machines. They are:
 
Operating
system 		  File name   Contents
linux/mac   rasscriptstart.scr   
#!/bin/csh
xterm -e /software/bin/rasmol -script $1
windows   rasscriptstart.bat   
"C:\Program Files (x86)\RasWin\raswin.exe" -script "%~1"
Edit the appropriate file to change the RasMol path to whatever it is on your computer.
 
Once you have installed all the required programs, and edited the CATHPARAM file as described above, you are ready to start running PDBsum1.
 
Instructions can be found in:
PDBsum1 Manual