Form Help

For a general introduction to 3D Blocks, please visit the introduction page.

Blocks Family IDs

A comma-separated list of family IDs from the Blocks database, e.g IPB000001,IPB000002.

User-supplied Blocks

Alignment data in Blocks format, such as from Blockmaker or the Blocks multiple alignment processor. Either paste in or upload a file or both. If you choose to paste in Blocks data and upload a Blocks file, make sure that no Block is found in both places.

Sequence alignment

A protein sequence alignment in FASTA, Clustal, or MSF format, which will be converted in to Blocks before being used.

PDB IDs

If you specify a comma-separated list of PDB IDs here, the specified Blocks will only be placed on those entries, and the entire PDB will never be searched.

Search cutoff

This cutoff in expect value is used to limit the PDB entries chosen from the database. The larger the expect value, the more entries will be found. The default of 10^-4 is fine for most situations. If you enter a value, it should be either in decimal form (e.g. 0.00001) or in scientific notation (e.g. 1e-15).

Maximum number of PDB Entries

Maximum number of PDB entries for which results will be displayed. The ones with the lowest expect values will be chosen. If the initial search of the PDB was a BLAST search rather than a MAST search, and more than sequence was used (i.e. more than one Blocks DB family was submitted, or the user supplied more than one sequence) PDB entries are chosen iterativelyfrom the results for each sequence so that an even distribution is created.

Don't Use BLAST

Determines if we do a BLAST search using one or more protein sequences to choose likely entries from the PDB or if we just do a MAST search on the entire database. The initial BLAST search is quicker, but may miss things.

Sequence

Sequences to use for an initial BLAST search. Only needed if you're supplying your own Blocks or an alignment; if you're using Blocks from the database, we'll use the COBBLER sequences unless you provide sequences here, in which case we'll use yours. If you provide sequences in both the file upload and paste in field, we'll use both, so make sure that no sequences appear in both places. If you supply more than one sequence, either by using both paste in and upload or supplying more than one sequence in either, the sequences will have to be in FASTA format so that we know where each one starts.

Last modified 8/23/02 by N. Taylor.