Morph Server FAQ
From Info
Frequently asked questions regarding the morph server
- If your question is not answered here, you can contact the administrator personally by mailing us.
Q.How realistic are these movies?
A. First, a disclaimer: these movies in no way represent what actually occurs during conformational change, although there are many cases where the real intermediates are probably quite similar. No time-scale/kinetic/dynamic information is known, and there may be additional states that have not been solved. The Morph Server is primarily a tool for informatics and scientific illustration, not a replacement for more crystallography or detailed (and time-consuming) MD simulation.
That said, the intermediate structures are usually fairly realistic, enough so to be indistinguishable in a molecular graphics program if not to PROCHECK. Energy minimization is kept to a minimum, but helps remove the most blatant distortions. The exceptions are a growing category of structures that undergo partial refolding or other massive transformations, such as the serpins or T7 polymerase, where a relatively linear pathway cannot be determined.
Q.I received an error message from the morph server. What happened?
A. There are several reasons why the server may fail. We've tried to make it obvious from the error message what exactly is wrong, but this isn't always very helpful, and the server isn't very well set up for debugging submissions. A few of the most common problems:
Conflicting SEQRES records. This is by far the most comment cause of failure! The server uses SEQRES data to determine the actual protein sequence. However, this frequently conflicts with the sequence intuited from ATOM records (including official PDB files from www.rcsb.org). If the server cannot automatically resolve these conflicts, it will fail. The easiest workaround to this is to submit files with SEQRES records deleted; if you supplied a PDB ID rather than a file you will need to download the proper file from the PDB, then modify and upload it. However, this may sometimes lead to other distortions, depending on the sequence numbering. Misformatted files. Although we're not sure of the exact details, files that do not have the standard Unix newline format usually are not parsed correctl. This is only a problem with user-submitted files, and can be fixed fairly easily with utilities such as dos2unix. (We'll probably modify the server to handle this too.) Incorrect parameters. If you enter a chain ID that is not present in the submitted files, this will result in an error when the server tries to fit the files. Server error. Sometimes we find (gasp!) bugs in the server. In these cases, we will of course attempt to fix the problem ourselves. Since the administrator receives notice of all morph failures, he is usually able to check and find out why the server quit.
