residue libraries

[foster.281]

Where can we find the residue libraries in NMRViewJ? The documentation I found point to a breslib folder that I could not find in the jar archives.

I'm asking because we need a residue library for a non-standard amino acid, and were looking for guidelines on how best to construct one.

Thanks!

-M

[brucej]

Once I started packing up NMRViewJ into the installers (in order to meet security requirements on Mac and Windows) the residue libraries got packaged into a .jar file.

To get them out, move to a directory where you want copies.

Locate the dcengineVersion.jar file within the installation directory.

Issue a jar command to extract them.  For example, on a Mac you would use:

jar xvf /Applications/NMRViewJ.app/Contents/Resources/app/lib/dcengine-9.2.0-b4.jar reslib_iu

Similar protocol on Linux or Windows, but the path to the "lib" directory containing the jar files will be different.

Note, jar is a command which is installed with the JDK (java development kit), and may not be present on your system.  But a .jar file is just a .zip file with a particular layout so you could also use unzip (or other unzipping program).

Once you create a new .prf file you can place it in a directory which will be searched prior to the default residue library.

I'll send info on that in a subsequent post.

Bruce

[brucej]

In the NMRViewJ Preferences Dialog there is a tab titled "Library".

In that, is a setting named "LocalResidues".

Enter the full path to a folder in that field. When reading in a sequence file NMRViewJ will look, for each residue name in the sequence file, for an entry in the local folder.  If it doesn't find one, it will look in the built-in residue library (stored in the dcengineVersion.jar file).  Thus, you can add new .prf files, or ones that replace existing ones with the same name.

Bruce