TGZ File

Files that have been compressed with gzip (GNU zip): Tar Gnu Zip (TGZ)

The TGZ files are sent by the STING server to a user after a job submission and processing is done in order to calculate all parameters for a local pdb-formatted file. This is a very important feature which allows a user to analyze local files containing model structures or newly deciphered structures.

Generally, STING operates with both PDB public files and local files in pdb format. However, in order to handle properly STING_DB parameters for a local file, STING needs to pre-calculate those. For this reason, we make available to a user two modes for handling local files:

1. a user can access some limited/reduced STING parameter list which are calculated typically in about 10-30 seconds. A user can get following STING components functioning:

2. Full list of STING parameters can be calculated and presented to a user if he/she first sends his/her local file in pdb format to the STING server, which in turn will process (in order of job deposition) and then send by e-mail a TGZ file to a user. This TGZ file will contain all STING parameters and can be used either for single file use (indicating a TGZ file as an input file to STING Millennium or JPD, or as a first/second structure of a pair to be aligned structurally in JPD).

A user is now able to get the full STING analysis of the local PDB-formatted files which are not part of the PDB.

Parameters calculated:
In BLUE STAR STING a user can get all the parameters calculated (except for the temperature factor and those linked to the HSSP) for the model structure or a new experimentally deciphered structure, not yet deposited to the PDB.

Time required for calculation:
However, as the calculation of ALL parameters is taking approximately 20 minutes for a PDB file of 200 amino acids, a user will be informed that the request will be handled by our server in a due time when his/her request comes to be executed by CRON. Namely, we have dedicated 4 CPUs for local file parameter calculation which allows for about 300 request being processed in 24 hours (counting average structure size of 200 amino acids).

Results obtained by e-mail in TGZ format:
The result will be sent to a user by e-mail in so called TGZ file (Tar Gnu Zipped file), containing all parameters calculated.

JPD and STING Millennium can use as input files the TGZ files:
Once having such file, a user can indicate it as an input file for JPD or STING Millennium and get immediately full parameter display for given structure.

Structurally Aligned local files and parameter calculation/display:
If a user desires to have structurally aligned files with accompanying structurally aligned parameters, this can also be done by processing two local files (one at the time) and then entering resulting TGZ files as input files in JPD. A combination of two local files, one local and one public as well as two public PDB files is possible. See more information on this particular subject here.