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homology modeling with threading says length mismatch between sequence and alignment

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homology modeling with threading says length mismatch between sequence and alignment
#1

HI,

I try to model my protein with two template PDBs. Later I learned that this kind of chimeric modeling hasn't been released yet. So I want to try to predict the structure of my protein with one scaffold PDB. But minirosetta says there is length mismatch. As I see there isn't length mismatch. Any comments? Thanks.

Here is what it spits out:
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...

ERROR: Error: length mismatch between sequence and alignmentproblem with sequence: 140734897977176 alignment: # score 456.789
t000_ 1 AAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDVLLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPILVSHNVYIMADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKGGTGGSMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNNPLNMNFELSDEMKALFKEPNDKALK
2VHA_A_renum 3 AAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFADLKGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWDIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPP-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KNLNMNFELSDEMKALFKEPNDKAL-
140734897977176
--

ERROR:: Exit from: src/core/sequence/SequenceAlignment.cc line: 289
0 libutility.dylib 0x00000001132f86a8 print_backtrace() + 40
1 libutility.dylib 0x00000001132f7a87 utility::exit(std::string const&, int, std::string const&, int) + 487
2 libcore.3.dylib 0x0000000110b2e5f2 core::sequence::SequenceAlignment::data_integrity_check() const + 320
3 libcore.3.dylib 0x0000000110b2e6ef core::sequence::SequenceAlignment::identities() const + 65
4 libprotocols_g.4.dylib 0x000000010c6a1999 protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(core::pose::Pose&, boost::shared_ptr<protocols::jd2::Job>) + 1223
5 libprotocols.1.dylib 0x000000010f6ec9b7 protocols::jd2::JobDistributor::run_one_job(boost::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool) + 1497
6 libprotocols.1.dylib 0x000000010f6ee4c3 protocols::jd2::JobDistributor::go_main(boost::shared_ptr<protocols::moves::Mover>) + 291
7 libprotocols.1.dylib 0x000000010f6c9349 protocols::jd2::FileSystemJobDistributor::go(boost::shared_ptr<protocols::moves::Mover>) + 65
8 libprotocols_g.4.dylib 0x000000010c66dc14 protocols::comparative_modeling::cm_main() + 100
9 minirosetta.default.macosgccrelease 0x00000001099a4267 main + 1351
10 minirosetta.default.macosgccrelease 0x00000001099a3a24 start + 52
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job 'S_2VHA_A_RENUM_0001'
Error:

Post Situation: 
Thu, 2015-08-06 11:46
rqliang

You are using a "general" alignment format.
Try this:
t000_ 1 --AAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDVLLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPILVSHNVYIMADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKGGTGGSMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNNPLNMNFELSDEMKALFKEPNDKALK
2VHA_A_renum 1 APAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFADLKGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWDIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPP-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KNLNMNFELSDEMKALFKEPNDKAL-

Good luck!

Sat, 2015-08-08 19:44
jharamesh

Since there is a huge gap in the template, and probably there is another template that would align well with your query sequence, an ideal protocol will be RosettaCM published in "Y. Song, F. DiMaio, R. Y.-R. Wang, D. Kim, C. Miles, T.J. Brunette, J. Thompson and D. Baker (2013) High resolution comparative modeling with RosettaCM. Structure. 21:1735-42."

It can be run using rosetta_scripts. Follow creation of .xml file and other input files discussed in the paper.

Sat, 2015-08-08 19:51
jharamesh