Sir(s), While trying to model my protein using Modeller 8v2, I encounter the following error message in the log file:
* Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = ted * I have checked the ALI and ATM files. Everything seems to be alright. Pls let me know what the problem could be.
Thanking you in advance. Madhan Kumar
*My alignment file:*
>P1;1ABC
structureX:1ABC:2 :O:231 :O::::
GGSDGLQDVTIMNQDQEQIIFAFPPVLGYGLMYQNLSSRLPS-YKLCAFDFIEE-EDRLDRYADLIQKLQPEGPLTLFGYSAGCSLAFEAAKKLEGQGRIVQRIIMVDSYKKQGVSDLDGRTVESDVEALMNVNRDNEALNSEAVKHGLKQKTHAFYSYYVNLISTGQVKADIDLLTSGADFDIPEWLASWEEATTGAYRMKRGFGTHAEMLQGETLDRNAGILLEFLNTQT*
>P1;ted
sequence:ted: :: :::::
------------------PVFVFHPAGGSTVVYEPLLGRLPADTPMYGFERVEGSIEERAQQYVPKLIEMQGDGPYVLVGWSLGGVLAYACAIGLRRLGKDVRFVGLIDAVRAG-----------------------------------------------------------------------------------------------------------------------*
*My script file:*
# Homology modelling by the automodel class
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = ''
a = automodel(env,
alnfile = 'align_ted.ali', # alignment filename
knowns = '1ABC', # codes of the templates
sequence = 'ted') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model
# (determines how many models to calculate)
a.make() # do the actual homology modelling
*Log file:*
** openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1ABC', 'ted'], atom_files=[], file='align_ted.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True)
openf___224_> Open align_ted.ali
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124923 2075.120 2.026
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2126623 2076.780 2.028
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2130023 2080.101 2.031
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2136823 2086.741 2.038
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2147161 2096.837 2.048 read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = ted