jitrayut jitonnom wrote: > and the PIR file of scfv is > >P1;scfv > sequence:scfv:1:L:123:H:::0.00: 0.00 > vmtqtpalmaaspgekvtitcsvsssisssnlhwyqqksetspkpwiygtsnlasgvpvrfsgsgsgtsysltis > smeaedaatyycqqwsnypltfgagtklelkssggggsggggggssrssl/evkllesggglvkpggslklscaas > gftfssyamswvrqtpekrlewvatissggtytyypdsvkgrftisrdnakntlylqmsslrsedtamyycarfr > ngaywgqgtlvtvsaatttapsv* > > After i run the script above i found some errros like this; > > read_al_373E> Protein specified in ALIGN_CODES(i) was not found > in the alignment file; ALIGN_CODES( 2) = scfv > > So, if anyone can help me for this problem i will be appreciated.

You have two problems:

1. Alignment files are case-sensitive. The 20 standard amino acids are all in upper case, not lower case.

2. Save your alignment file in plain text. While the file here looks OK, the attachment you sent separately is formatted as Rich Text Format. If you make the file in a text editor in Windows, make sure when you save the file, you select "plain text" format.

Ben Webb, Modeller Caretaker