ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different
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
On 7/16/12 2:59 PM, Jonathan Crane wrote: > 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.
You have your chains the wrong way round.
You have asked Modeller to read everything from the start of the H chain to the end of the L chain, but Modeller simply reads residues as they are presented to it in the PDB, and 1u6a has the L chain *before* the H chain. So Modeller happily skips all of the L chain to find residue 2:H before it starts reading, and then it reads all the way to the end of the H chain before stopping (since it never finds 215:L). Either swap the chains in your alignment file, or edit the PDB file to put them in the desired order.
Ben Webb, Modeller Caretaker
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Jonathan Crane -
Modeller Caretaker