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Adding Sequences

Adding Sequences

From a FASTA file

There are several ways to add Protein, DNA or RNA sequences to your project. The easiest is simply to drag and drop a FASTA file into the sidebar or drop area (make sure the file extension is .fasta). Alternatively, you can go to File / Load Data or Molecules / Chain from FASTA... to select and read in a FASTA file. Analysis will then automatically generate a Chain and Substance for you which will be listed in the sidebar. To change the name of your Substance or the ChainCode, simply double-click on the Substance or Chain in the sidebar and you can make your changes in the Edit Substance or Edit Chain pop-ups.

Manual addition of a sequence

If you prefer to type or copy & paste your sequence into the program, then you can go to Chain in the sidebar and double-click on New Chain or select New Chain... from the Molecules menu. This brings up a pop-up. Enter the Chain Name, the Molecule Name (this is the name listed under Substances and can be changed later by double-clicking on your Substance in the sidebar), select the Molecule Type (protein, DNA, RNA, other) and set the number at which the sequence starts.

You can enter your sequence in either the standard One-Letter Code format (A for alanine etc.), the Three-Letter Code format (ALA for alanine etc.) or using the Ccp Code format (Ala for alanine etc.). The sequence can be entered space or comma separated. For 1- and 3-letter codes, the sequence can also be entered as a single string and there is no need to be case sensitive. The sequence will be automatically formatted into blocks of 10 residues with numbering, and any incorrect or unidentified residue types will be highlighted in red with a box around them. Use the two buttons below the sequence entry box to switch the sequence format between a plain text block (orange back arrow) and validated blocks of 10 (refresh arrow with numbers). If you wish, you can right-click on your sequence and select Copy all to Clipboard as 1Letter/3Letter/CcpCodes and then paste this into another tab or elsewhere on your computer. The Ccp Code entry is intended mainly for those working with non-canonical amino acids. See our page on Creating Chains with non-canonical amino acids for more information on this.

There are then a number of additional options you can select which do the following:

Once you have clicked OK, your sequence and molecule will show up in the Chains and Substances part of the sidebar. The sequence will also appear in the Residue Information (RI) and Sequence Graph (SG) modules.

If your protein or peptide Chain contains non-canonical amino acids, you may wish to look at our page on Creating Chains with Non-canonical Amino Acids.

Clone a sequence

If you are working with a homodimer, you may need to have two Chains of the same protein in your project. You can add an exact copy of a Chain by right-clicking on a Chain and selecting Clone. This adds an additional Chain, but no further Substance to your project.

Adding a similar sequence

If you want to add a second Chain which is similar, but slightly different to an existing one (e.g. a mutant or a slightly longer/shorter construct), then you can right-click on a Chain and select New Chain from selected.... This will open the New Chain pop-up, but will pre-fill it with the sequence and other details from the starting Chain. You can now make any changes you require and create your new Chain. By default, the sequence will be shown in the Ccp Code format, but remember that you can always copy it into 1- or 3-letter format if you wish.

The New Chain from selected... function is also useful if you made a mistake in your original Chain which you want to correct. At the moment it isn't possible to edit Chains directly, but this function hopefully makes it easy to create a new corrected Chain quickly and easily.