I have completed the tutorial successfully to 3rd script. Then later when I was running my fourth script this error pops up saying “IOError; pdbnam______E> Filename for PDB code not found: tseq1 .pdb
Directories:
Extensions : ;.atm;.pdb;.ent;.cif;.crd……..
I have followed all your query answers and couldn’t find a solution. I have placed all my file sin the working directory and also hav all the pdb files requies in the working folder but still why couldn’t modeller read the pdb file specified….help greatly greatly appreciated.
Filename for PDB code not found: tseq1 .pdb
The space between tseq1 and .pdb maybe? Perhaps you can attach or paste the 4th script to make us easier in troubleshooting your problem.
Regards,
Radif
from modeller import *
from modeller.automodel import *
#from modeller import soap_protein_od
env = environ()
a = automodel(env, alnfile='qseq1-tseq1.ali',
knowns='tseq1', sequence='qseq1',
assess_methods=(assess.DOPE,
#soap_protein_od.Scorer(),
assess.GA341))
a.starting_model = 1
a.ending_model = 5
a.make()
Alright, check your *.ali file. and see if there is any pdb filename below >P1;tseq1 (see the picture below). And make sure the pdb filename is the same to the pdb file in the folder. I suspect that the name below the >P1;tseq1 is incorrect.
i solved the problem. You are partially right Muhammad Radifar but the name in the script and the name in the alignment file were different hence this problem arised. Thank you for your answer.
The mistake is marked in bold
from modeller import *
from modeller.automodel import *
#from modeller import soap_protein_od
env = environ()
a = automodel(env, alnfile='qseq1-tseq1.ali',
knowns='tseq1A', sequence='qseq1',
assess_methods=(assess.DOPE,
#soap_protein_od.Scorer(),
assess.GA341))
a.starting_model = 1
a.ending_model = 5
a.make()
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