[modeller_usage] (no subject)

[Markus Heller <>]

Hi,

I'm trying to model two missing loops in a homo-dimeric protein, following the example on the web: https://salilab.org/modeller/wiki/Missing%20residues

I have saved chains A and C (forming the dimer) as pdb, and then extracted the sequence using get_seq.py (see below).  Then I created an alignment file and inserted the missing residues to give the alignment file shown below.

When I try to do the modeling, I get a "KeyError: 'No such residue: 346:B'" (see calc_model.py below).  I've tried to rename the chains in my script.

What's my mistake?

Thanks and Cheers
Markus

%%%%%%%%%%%%%%%%%%%%%% calc_model.py %%%%%%%%%%%%%%%%%
from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()

env = environ()

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

class MyModel(automodel):
    def special_patches(self, aln):
        # Rename both chains
        self.rename_segments(segment_ids=['A', 'B'])

    def select_atoms(self):
        return selection(self.residue_range('346:A', '350:A'),
                         self.residue_range('346:B', '348:B'))

a = MyModel(env, 
            alnfile = 'alignment.ali',
            knowns = '4yng_AC',
            sequence = '4yng_AC_fill')

a.starting_model= 1
a.ending_model  = 5

a.make()
%%%%%%%%%%%%%%%%%%%%%% end of calc_model.py %%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%% alignment.ali %%%%%%%%%%%%%%%%%
>P1;4yng_AC
structureX:4yng_AC:   1 :A:+932 :C:MOL_ID  1; MOLECULE  PYRUVATE KINASE I; CHAIN  A, B, C, D, E, F, G, H; SYNONYM  PK-1; EC  2.7.1.40; ENGINEERED  YES:MOL_ID  1; ORGANISM_SCIENTIFIC  ESCHERICHIA COLI; ORGANISM_TAXID  562; GENE  PYKF, Z2704, ECS2383; EXPRESSION_SYSTEM  ESCHERICHIA COLI BL21(DE3); EXPRESSION_SYSTEM_TAXID  469008: 2.28: 0.22
MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVMSKTGKTAAILLDTKGPEIRTM
KLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGLIGMEVTAIEGNKVICKVLNNG
DLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIREHLKAHGGENIHIISKIENQE
GLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQMLDSMIKNPRPTRAEAGDVAN
AILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEF-----KLRITEAVCRGAVETAEKLDAPLIV
VATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHKGDVVV
MVSGALVPSGTTNTASVHVL/MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVM
SKTGKTAAILLDTKGPEIRTMKLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGL
IGMEVTAIEGNKVICKVLNNGDLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIR
EHLKAHGGENIHIISKIENQEGLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQ
MLDSMIKNPRPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEF---NRKLRI
TEAVCRGAVETAEKLDAPLIVVATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDF
YRLGKELALQSGLAHKGDVVVMVSGALVPSGTTNTASVHVL*

>P1;4yng_AC_fill
sequence:::::::::
MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVMSKTGKTAAILLDTKGPEIRTM
KLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGLIGMEVTAIEGNKVICKVLNNG
DLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIREHLKAHGGENIHIISKIENQE
GLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQMLDSMIKNPRPTRAEAGDVAN
AILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEFNNDNRKLRITEAVCRGAVETAEKLDAPLIV
VATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHKGDVVV
MVSGALVPSGTTNTASVHVL/MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVM
SKTGKTAAILLDTKGPEIRTMKLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGL
IGMEVTAIEGNKVICKVLNNGDLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIR
EHLKAHGGENIHIISKIENQEGLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQ
MLDSMIKNPRPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEFNNDNRKLRI
TEAVCRGAVETAEKLDAPLIVVATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDF
YRLGKELALQSGLAHKGDVVVMVSGALVPSGTTNTASVHVL*
%%%%%%%%%%%%%%%%%%%%%% end of alignment.ali %%%%%%%%%%%%%%%%%