The calculation of the different Secondary Structure elements in a protein structure, is mostly done using the DSSP program by Kabsch and Sander. The output of this program is the product of extensive calculations and sometimes very hard to understand for people that are not familiar with its usage.
Using this server you can submit a Protein Structure file and get a formatted output of the Secondary Structure Elements calculated by DSSP and some other useful features of the protein like the accessible residues, the residues involved in a symmetry contact with other residue in some of the other molecules in the crystal.
In the fisrt case we will check for the availability or this PDB structure in our PDB directory, and we will check in the PDB_REPORT if this file is deemed to be good and can be read with WHAT_IF (there are some structures that have too many problems), If everything is OK, we will run WHAT_IF and DSSP on the Structure and you will have the results directly on your browser.
The second method is much more simple, we will get your file and run directly WHAT_IF and DSSP on it.
Note: We are using the File Upload mechanism described in
RFC 1867,
this mechanism has been implemented in Netscape from version 2.0 up.
If you are using any Netscape version above 2.0 and you receive an error
message immediately after clicking the "send the files" button, then try again
after having disabled the Netscape Proxy option.
Oh! by the way if you have the litle mistake of sending a directory instead of a file, you will not get the next page inmediately, instead, the browser will say that is contacting us, but it will take almost forever.
If you want to save time sending long files, you can compress them using the standard UNIX compress or GNU gzip