Import Window : Edit Commands

The items in this menu mostly have the same meaning as they do in the Sequence Window : Edit menu, with a few additions:

• Delete all blocks
• Delete all blocks in all alignments
• Sort imports
• Import sequences
• Import structure

Delete all blocks

Delete all blocks in all alignments

Sort imports

Sorts imports by:

• Sequence identifier: (of the imported sequence), putting PDB sequences at the top in alphabetical order, followed by non-structured sequences in numerical order of their identifier.
• PSSM score: sorts rows by the sum of the residue-to-PSSM scores for all aligned residues, with the highest at the top.

Import sequences

Use this item to import new sequences. You will be given a choice to import multiple sequences from a FASTA file, or a single sequence from NCBI via the network. The new sequences will be imported without an alignment. It will then be up to you to align the sequences manually or with one of the available algorithms.

Import structure

Allows you to import a new structure and the sequence of the aligned chain. You will be given a choice whether to import from a file or directly from NCBI via the network; if you import from a file, the structure must be of the type downloaded from the MMDB server, and must be of the right all-atom or alpha-only type to match the existing structures. After the structure is loaded, Cn3D will query the VAST database to see whether a structure alignment exists; if so, it will load both the structure alignment and the corresponding sequence alignment. If VAST has no alignment for the two chains, the sequence will be imported without any alignment, and you'll have to align it manually or using one of the built-in alignment algorithms.

Note that the structure will not appear right away. You must first save the data to a file, and then re-load. And if there is an existing multiple alignment already, depending on the data type the structure may not be visible until after you merge the new sequence into the multiple alignment.