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[modeller_usage] error message



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