In the "Protein" box at the top of the form, you can enter a uniprot squence identifier (such as P01112 or RASH_HUMAN), or paste a sequence into the box. In general, this should be the complete protein sequence, even if you intend to compute structure only for a part of the protein (a domain). If you know that your protein is a transmembrane domain, set "Is Membrane" to "Yes".
If not, leave this blank. Otherwise, enter the pdb identifier for "Known Structure", for example "5p21". The known structure will be used for comparison only (not guiding structure calculations).
Give your job a name. This name will be attached to result filenames and used as a default name in certain cases (for instance, if you pasted in a protein sequence, this will become the sequence identifier).
Jobs may take a long while to complete. We will email you a notification when the job does complete, or if it stops before completion.
When you are ready to Launch the job, use the Launch button at the bottom of the page. The job will be queued for processing if there are no problems or missing pieces. Once the job is queued, you will receive an email notification that the job had been submitted. If this is the first job you have launched on our sever, you will first get an email with a web URL to click on to validate your email address. The email will contain a link to the job status page, showing how far the processing has progressed. When the job is complete, you will receive a second email message with links to the results.
By default, we will generate a multiple sequence alignment for your protein, using the complete protein sequence. If the structure computation should be focussed on a particular domain within the protein sequence, you will need to guide the alignment generation stage (HHblits/jackhmmer) by entering the residue offsets for the beginning and end of the domain (relative to the complete protein sequence). That can be done under the advanced settings section "Alignment Generation / Selection".
Multiple sequence alignments are generated on the server using HHblits or jackhmmer. It may be that the alignment which is generated has too few members ... or too many which are only weakly related to your sequence of interest. You can tune the inclusiveness of the generated alignment with the E-Value parameter under the section "Alignment Generation / Selection".
If you want to use an existing multiple sequence alignment (either your own, or a retrieved one) instead of a generated one, you can do that under the "Alignment Generation / Selection" section.
The number of top ranking EC's to be applied during structure calculations will be set by default to a few values near the residue length of the sequence. Contact maps will be plotted with these default EC counts as well. But you can alter the counts of ECs to be used and also adjust the contact map plotting parameters under the sections "Number of Evolutionary Constraints / Number of Structure Variants" and "Contact Maps / Comparing Computed Structure to PDB Known Structure".
There are quite a few other settings, but if you don't run into problems and are not interested in exploring the effects of manipulating various low level details, you can ignore them.
When your job is complete, you will be able to download the results as a gzipped tar file. Inside that file will be:
Also the results download will contain files used as input into cns_solve, including:
Additional files may be present, such as lists of calculated structures, degree of energy minimization, and MATLAB figure formatted contact maps.