Hello.
Here is my script (for MODELLER6v2):
INCLUDE
SET ATOM_FILES_DIRECTORY=''
SET ALNFILE='GPR43_ES_HSA#2.ali'
SET KNOWNS='rhodo_1u19'
SET SEQUENCE='GPR43_ES_HSA'
SET OUTPUT_CONTROL=1 1 1 1 1
SET STARTING_MODEL=1
SET ENDING_MODEL=1
CALL ROUTINE='model'
#Redefine the special_restraints routine to disable energy optimization on the residues 123 to 143
SUBROUTINE ROUTINE='special_restraints'
DELETE_RESTRAINT RESIDUE_IDS='123' '124'
END_SUBROUTINE
#energy optimization
ENERGY OUTPUT='SHORT'
OPTIMIZE OPTIMIZATION_METHOD=1,MAX_ITERATIONS=10
But I when I run the script, here is the error message :
No ":" in ATOM:RESID[CHAINID] atom identifier
I have replaced several times the string after 'RESIDUE_IDS=' ( for example: '123 :','124 :' ), but it doesn't change anything.
Thanks by advance.
Ludovic PETAIN
EUROSCREEN SA
Tel +32 71 348 500
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Direct +32 71 348 5XX
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Ludovic Pétain wrote: > Here is my script (for MODELLER6v2):
I strongly recommend you use a newer version of Modeller. 6v2 is very old.
> DELETE_RESTRAINT RESIDUE_IDS='123’ ‘124'
DELETE_RESTRAINT takes ATOM_IDS, not RESIDUE_IDS. For example, you might say
DELETE_RESTRAINT ATOM_IDS = 'O:56' 'C:56' 'N:57' 'CA:57'
to remove any restraint on the given dihedral. See http://salilab.org/modeller/6v2/manual/node105.html and http://salilab.org/modeller/6v2/manual/node104.html
Ben Webb, Modeller Caretaker
Hi there,
I am new to modeller and I have trouble creating a homology model of a protein using two templates. I modified the model-default.py script as shown below and I got error messages. I would appreciate it if any one can give me any suggestion.
Thanks. Thomas
Here is model-default.py script I am using: ##################################################################### # 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 = './:../atom_files'
a = automodel(env, alnfile = 'alignment1.ali', # alignment filename knowns = '2MDbis 1wu9', # codes of the templates sequence = 'flq15691') # 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
#########################################################################
my alignment file looks: ################################################################### >P1;2MDbis structureX:2MDbis:1 : :148 : :Eb1:Homo sapience: 1.90: 0.19 ..... >P1;1wu9 structureX:1wu9:A : :59 : :Eb1:Homo sapience: 1.90: 0.19 ...... >P1;flq15691 sequence:flq15691:1: :286::q15691:Homo sapience: 2.00: -1.00 ...... #####################################################################
I am getting the following error message ######################################################################## Traceback (most recent call last): File "model-default.py", line 18, in ? a.make() # do the actual homology modelling File "/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py", line 318, in homcsr aln = self.read_alignment() File "/usr/local/programs/modeller-8v2/modlib/modeller/automodel/automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/usr/local/programs/modeller-8v2/modlib/modeller/alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "/usr/local/programs/modeller-8v2/modlib/modeller/alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "/usr/local/programs/modeller-8v2/modlib/modeller/util/top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = flq15691 ###################################################################
Thomas K. Weldeghiorghis wrote: > I am new to modeller and I have trouble creating a homology model of a > protein using two templates. I modified the model-default.py script as > shown below and I got error messages. I would appreciate it if any one > can give me any suggestion.
> a = automodel(env, > alnfile = 'alignment1.ali', # alignment filename > knowns = '2MDbis 1wu9', # codes of the templates > sequence = 'flq15691') # code of the target
'knowns' is an ordinary Python list, so should be: knowns = ('2MDbis', '1wu9')
See the multiple template example in the advanced tutorial for more information: http://salilab.org/modeller/tutorial/advanced.html
Ben Webb, Modeller Caretaker
-
Ludovic Pétain -
Modeller Caretaker -
Thomas K. Weldeghiorghis