PLCC_from_shell

Running PLCC from the shell prompt

PLCC and SplitPBD are programs which were designed to be run in batch mode for thousands of input files (e.g., the whole PDB). This means they are command line programs, so you will have to run them from a shell prompt. This page explains in detail howto do that. It is intended for people who are very new to the command line.

Part 1: Installation (all Operating systems)

1.1 Download and unzip the VPLG release

For the instructions below to work, download a VPLG release (latest is always best). It should be a zip file, name vplg_2015_02_02.zip or similar. Extract the vplg folder from the ZIP archive. For this howto, I will assume you have put it in your Downloads directory.

Here you can see the contents of the extracted vplg directory (Win7):

1.2 Install Java (if you do not have it already)

If you do not have Java installed already, install it now from https://java.com/download.

In case you are unsure whether you have it, don't worry. We will ensure it is installed properly before running VPLG. If it turns out that Java is not properly installed, you can still install it.

Part 2: Running PLCC from the shell -- Linux / MacOS / Cygwin

Start a shell (sometimes also called command prompt or terminal) from your operating system. You should be in your user home then, and it should look roughly like this (Cygwin):

OK, let's get started. In this tutorial, we are going to copy some example input data (that comes with VPLG) to the run directory, and run PLCC using this data. The commands you should type are in bold, the output is normal font.

2.1 Check whether java is installed properly:

**java -version**

This should produce output like the following:

If it gives you an error message (e.g., command not found), Java is not installed properly and PLCC cannot work. In that case, install Java now (see 1.2 above).

2.2 Change to your vplg directory

Remember, I assume it is Downloads/vplg/

**cd Downloads/vplg/**

2.3 Get input data for PLCC

Copy the data to the current directory (you could use it from elsewhere too, but it is easier this way). Some PDB and DSSP example files come with VPLG. They can be found in the exampledata/input/ directory. Let us copy the data for 7tim to our working directory:

**cp example_data/input/7tim.* .**

You should now see the files 7tim.pdb and 7tim.dssp in the current directory if you list the contents using the command ls:

2.4 Run PLCC

Run plcc on the data for 7tim. This is straight-forward:

**java -jar plcc.jar 7tim**

The output is quite long. It should look roughly like this:

plcc -- Protein-Ligand Contact Calculation
Init... (Version 0.97)
Loaded 124 settings from properties file.
Starting computation for PDB ID '7tim' at 2015/09/16 19:05:45.
Using PDB file '7tim.pdb', dssp file '7tim.dssp', output directory '.'.
Checked required files and directories, looks good.
Not using the database as requested by options.
Getting data...
Reading files...
Read 4526 lines of file '7tim.pdb'.
Read all 523 lines of file '7tim.dssp'.
Parsing pdb and dssp file lines...
Scanning whole PDB file for models...
Counting total number of models in the whole PDB file '7tim.pdb' (4526
lines)...
PDB: Scanned whole PDB file for Models, found 0.
PDB: This most likely is crystal data (a non-NMR file without models). A
default model will be created.
Creating all Models from handled PDB lines...
PDB: Handled PDB lines contain data from 1 model(s).
Creating all Chains...
PDB: New PDB Chain (chain ID 'A') starts at PDB line 470.
PDB: New PDB Chain (chain ID 'B') starts at PDB line 2354.
PDB: Scanned PDB file for Chains, found 2.
Creating all Residues...
DSSP: Found start of DSSP data in line 29.
DSSP: Found chain brake at DSSP line 276.
Creating all Ligand Residues...
PDB: Added ligand 'PGH-249', chain A (line 4238, ligand #1, DSSP #496).
PDB: => Ligand name = 'PHOSPHOGLYCOLOHYDROXAMIC ACID', formula = '2(C2 H6
N O6 P)', synonyms = ''.
PDB: Added ligand 'PGH-249', chain B (line 4248, ligand #2, DSSP #497).
PDB: => Ligand name = 'PHOSPHOGLYCOLOHYDROXAMIC ACID', formula = '2(C2 H6
N O6 P)', synonyms = ''.
Creating all SSEs according to DSSP definition...
Creating all Atoms...
PDB: Found C Terminus of chain A at PDB line 2353, PDB residue number 248
iCode ' '.
PDB: Found C Terminus of chain B at PDB line 4237, PDB residue number 248
iCode ' '.
PDB: Hit end of PDB file at line 4526.
PDB: Selecting alternative locations for atoms of all residues.
PDB: Deleted 0 duplicate atoms from 0 residues which had several alternative
locations.
All data parsed. Found 1 models, 2 chains, 496 residues, 3786 atoms.
PDB: Found the following NMR models in the whole PDB file:
PDB: <None> (No NMR data, an artificial default model was added.)
DSSP: Protein contains no disulfide bridges.
Maximal center sphere radius for all residues is 71.
Maximal distance between residues that are sequence neighbors is 677.
Received all data (1 Models, 2 Chains, 496 Residues, 3786 Atoms).
Calculating residue contacts...
Checked 122760 contacts for 496 residues: 7978 possible, 2155 found, 114782
impossible (collison spheres check).
Did not check 0 contacts (skipped by seq neighbors check), would have been
122760.
Received data on 2155 residue contacts that have been confirmed on atom level.
Not writing any interim results to text files as requested (geom_neo
compatibility mode off).
Calculating SSE graphs.
Calculating SSEs for all chains of protein 7tim...
+++++ Handling chain 'A'. +++++
Retrieved all meta data for chain 'A' from PDB header.
Creating all SSEs for chain 'A' consisting of 248 residues.
Added 1 ligand SSEs to the SSE list, now at 22 SSEs.
SSEs: EHEHEHEHHEHHEHHHEHEHHL
----- Calculating albe graph of chain A. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_A_albe_PG.png) (SVG =>
.\7tim_A_albe_PG.svg) (PDF => .\7tim_A_albe_PG.pdf)
Not handling folding graphs.
----- Calculating albelig graph of chain A. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_A_albelig_PG.png) (SVG =>
.\7tim_A_albelig_PG.svg) (PDF => .\7tim_A_albelig_PG.pdf)
Not handling folding graphs.
----- Calculating alpha graph of chain A. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_A_alpha_PG.png) (SVG =>
.\7tim_A_alpha_PG.svg) (PDF => .\7tim_A_alpha_PG.pdf)
Not handling folding graphs.
----- Calculating alphalig graph of chain A. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_A_alphalig_PG.png) (SVG =>
.\7tim_A_alphalig_PG.svg) (PDF => .\7tim_A_alphalig_PG.pdf)
Not handling folding graphs.
----- Calculating beta graph of chain A. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_A_beta_PG.png) (SVG =>
.\7tim_A_beta_PG.svg) (PDF => .\7tim_A_beta_PG.pdf)
Not handling folding graphs.
----- Calculating betalig graph of chain A. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_A_betalig_PG.png) (SVG =>
.\7tim_A_betalig_PG.svg) (PDF => .\7tim_A_betalig_PG.pdf)
Not handling folding graphs.
+++++ All 6 protein graphs of chain A handled. +++++
+++++ Handling chain 'B'. +++++
Retrieved all meta data for chain 'B' from PDB header.
Creating all SSEs for chain 'B' consisting of 248 residues.
Added 1 ligand SSEs to the SSE list, now at 21 SSEs.
SSEs: EHEHEHEHHEHHEHHEHEHHL
----- Calculating albe graph of chain B. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_B_albe_PG.png) (SVG =>
.\7tim_B_albe_PG.svg) (PDF => .\7tim_B_albe_PG.pdf)
Not handling folding graphs.
----- Calculating albelig graph of chain B. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_B_albelig_PG.png) (SVG =>
.\7tim_B_albelig_PG.svg) (PDF => .\7tim_B_albelig_PG.pdf)
Not handling folding graphs.
----- Calculating alpha graph of chain B. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_B_alpha_PG.png) (SVG =>
.\7tim_B_alpha_PG.svg) (PDF => .\7tim_B_alpha_PG.pdf)
Not handling folding graphs.
----- Calculating alphalig graph of chain B. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_B_alphalig_PG.png) (SVG =>
.\7tim_B_alphalig_PG.svg) (PDF => .\7tim_B_alphalig_PG.pdf)
Not handling folding graphs.
----- Calculating beta graph of chain B. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_B_beta_PG.png) (SVG =>
.\7tim_B_beta_PG.svg) (PDF => .\7tim_B_beta_PG.pdf)
Not handling folding graphs.
----- Calculating betalig graph of chain B. -----
Exported protein ligand graph in 8 formats (gml tgf gv kavosh el plg json
xml ) to 'E:\ts_home\downloads\vplg.\'.
Output protein graph files: (PNG => .\7tim_B_betalig_PG.png) (SVG =>
.\7tim_B_betalig_PG.svg) (PDF => .\7tim_B_betalig_PG.pdf)
Not handling folding graphs.
+++++ All 6 protein graphs of chain B handled. +++++
All 2 chains done.
All done, exiting.

2.5 Check the results

Now, the protein graph files should be in the current directory. Once more, let us check directory content with the ls command:

That's a lot of output files! Let us open one of the output files, 7tim_A_albe_PG.png, with your favourite image viewer/editor software. (No need for the shell anymore, just navigate to the directory in your file manager and double-click the image file):

That's it. You have successfully run plcc from the command line.