[modeller_usage] ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different

[Jonathan Crane <>]

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