Version 1.4.5 includes the program "alsnum". This is a temporary solution to the residue numbering problem. Ultimately, these functions will be included as alscript commands.
alsnum creates a set of TEXT commands that can be incorporated into an alscript command file to place sequential numbers at any position in the alignment. The numbers ignore gaps, so the numbering will correspond to the specific sequence position rather than the alignment.
To use the program:
1. Decide where you want the numbers to be placed. For example, you might want the numbers above the third sequence in the alignment. If so, make an extra sequence space above the third sequence using the ADD_SEQ command.
2. Decide what is the number of the first residue of the sequence to be numbered. This will not always be 1 since you may be aligning fragments or domains.
3. Decide the numbering interval (e.g. every 10th amino acid).
4. Run the program.
For example, if you want to add numbers according to sequence 37 of a block file (junk.blc), calling the first residue of the sequence 12, and with an interval of 5, and the numbers are to be placed at the location of sequence 3 in the alignment. Type:
alsnum 37 12 5 3 < junk.blc > junk.text
5. Add the resulting TEXT commands from junk.text to your alscript command file.