How to create your own post-download conversion / processing activity

In this topic we will go through the steps explaining how to create your own user-specific post-download conversion / processing activity. In the previous topic we saw that the activity can be accomplished with a console background application such as xml2pdb.exe. Other examples of the console-background-application activity are zipping/unzipping file archives with zip.exe, rar.exe, gzip.exe, Minigzip.exe, or file processing with numerous bioinformatics tools / utilities, or your own application (Perl scripts, Python scripts, binaries, etc.)

We would like to emphasize that the activity should not be limited only to console-based applications. Here we present an activity that opens every PDB file one-by-one with a molecular graphics visualization program, RasMol. The goal of the activity is to visually get acquainted with every PDB structure from the list. The user can also specify the maximum time allocated for viewing every structure in RasMol.

Instead of RasMol it can be any graphical user interface (GUI) application that accepts a PDB or other bioinformatics file as input argument. The user might consider such way of using the post-download conversion / processing tool as means of considerable time saving from routine repeatable actions done with each downloaded file.

Creating an activity: 3D viewing of a set of structures with Rasmol

1) In the Main toolbar of BioDownloader click Convert button or Main Menu → Tools → Convert.

2) The docked Files conversion window will be shown:

3) Specify raswin.exe as Executable:

4) Define the path of the directory with the input PDB files:

5) Enter the desired file Mask of the files you want to view in Rasmol:

6) Browse for the Output (working) directory:

7) Enter the following in Executable argument line:

This field specifies what argument line is passed to the application, in this case to raswin.exe.

As the first argument we want to specify the full-path filename of a pdb file from the list. Thus, we type in %FULLNAME. In its turn %FULLNAME is a result of merging of %IDIR and %INAME. %IDIR is the path of the folder containing the input files. %INAME is substituted with any filename satisfying the Mask. (We don't want to put simply %INAME as the first argument because those files are stored in a location different from the Output (working) directory.)

It is a set of Rasmol commands that we want to apply in every Rasmol session.

8) Choose how many seconds you would like to spend for each PDB file:

If you enter 15 seconds then every 15 seconds the structure in Rasmol Viewer is switched to the next one in the list. If you close Rasmol Viewer with the current structure before the timeout has expired then the next structure from the list will be shown. If you want to spend almost unlimited amount of time per each structure then enter the maximum possible value. The default value is 180 seconds.