This form allows you to upload a PDB-formatted file and generate all STING_DB parameters for a structural analyses to be done by the JPD, STING_Report etc.. (For released PDB entries the STING_DB has already generated all parameters in synchronicity to the PDB updates - so please access these via the STING page for a public PDB files).
The structure you are submitting, and its STING_DB parameters which you are requesting to be calculated, will be sent to you via e-mail.
No other user can be accessing your data, however, we do not guarantee the total security due to the e-mail related security issues.
After you submit the file with a structure to the STING server, this file will be assigned a STING_Que identifier. It will be then placed in a queue for the next STING_DB local file parameter generation run. At this moment, the processing occurs every day between 9 PM and 7 AM (Standard Brasilia Time : for the reference and comparison with your local time, please consult the : http://www.timeanddate.com/worldclock ) on 4 CPUs of our STING public server (SGI UV 2000). Approximately 300 files can be processed per day assuming average protein size of 200 amino acids.
When the run is complete you will be e-mailed your TGZ file.
The name of the file would be the TENTATIVE FILE NAME you indicated at the entry form.
The sender would be STING_info.
You can then access any of the STING mirrors and designate the TGZ file as an input file to either JPD or STING Millennium.
Users often report that the TGZ generation was not successful, assuming that the STING server is in fault. In fact in most cases, we are found to debug users PDB format file which is inapropriate and causes errors during the TGZ execution.
Types of errors we most frequently encounter are as follows:
1. Formating AA sequence number (double occupancy)
ATOM 80 N AGLN A 11 12.269 13.227 38.632 0.50 16.39 (wrong)
ATOM 80 N GLN A 11A 12.269 13.227 38.632 0.50 16.39 (correct)