Hi, I am trying to model a 2-chain Ab sequence, but I keep getting the same error. I think it is not reading the chain break '/' correctly, but not sure. Here's the ali text:
>P1;1U6A structure:1U6A:2:H:215:L:antiGP120:human:2.81:-1.00 -VQLQESGPGLVKPSETLSLTCTVSGGSISSHYWSWIRQSPGKGLQWIGYIYYSGSTNYSPSLKSRVTISVETAKNQFSLKLTSMTAADTAVYYCAR--GPVPAVFYGDYRLDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP/EIVLTQSPGTLSLSAGERATLSCRASQSVSSRYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRVEPEDFAVYYCQQYDNSVCTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE*
>P1;rAb53 sequence:rAb53:2:H:215:L:rAb53mod:human:-1.00:-1.00 QVQLQESGAGLVKPSETLSLTCTVSGGSISGHYWNWIRQPPGKGLEWIGYIHYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARAEGRGWSAFY-YYYMEVWGKGSTVSVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP/EIVLTQSPGTLSLSAGERATLSCRASQSVSSRYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRVEPEDFAVYYCQQYDNSVCTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE*
and the log result: read_te_290E> Number of residues in the alignment and pdb files are different: 436 222 For alignment entry: 1 1U6A x (mismatch at alignment position 223) Alignment YICNVNHKPSNTKVDKKVEPEIVLTQSPGTLSLSAGERATLSCRASQSVSSRYLAWYQQKP PDB YICNVNHKPSNTKVDKKVEP Match ********************
It looks like the PDB ends after the heavy chain instead of reading after the chain break and including the light chain, but I can't figure out why. Any ideas? Thanks Jon