Subject: [modeller_usage] 1st time trying modeller
From: Irene Newhouse <>
Date: Wed, 17 Nov 2010 09:07:20 -1000
Priority: normal
I'm trying to get the format right for a multiple alignment I did with a Clustal W server to use as input to modeller. I don't understand the error message; it probably means I don't understand the numbering convention. My sequence has 290 residues & ends up with 316 characters due to alignment gaps. I get exactly the same error message whether I use 290 or 316 as the end residue. Below are various bits of information that might be helpful in debugging what I'm doing.
Thanks for your help! Irene Newhouse
***The input python script: [newhoir@localhost rubber]$ cat mod-rubber1.py # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes 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 = ['.', '/home/newhoir/rubber/atom_files']
a = automodel(env, alnfile = 'multi.ali', # alignment filename knowns = ('2d2r', '1ueh', '2vg3', '1f75', '2vg0'), # codes of the templates sequence = '2cpt') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling
***The run command: mod9v8 mod-rubber1.py
***atom_files: ls -l /home/newhoir/rubber/atom_files total 2640 -rw-rw-r-- 1 newhoir newhoir 324891 Nov 16 11:17 1f75.pdb -rw-rw-r-- 1 newhoir newhoir 405810 Nov 16 11:18 1ueh.pdb -rw-rw-r-- 1 newhoir newhoir 372276 Nov 16 11:19 2d2r.pdb -rw-rw-r-- 1 newhoir newhoir 707778 Nov 16 11:18 2vg0.pdb -rw-rw-r-- 1 newhoir newhoir 862326 Nov 16 11:18 2vg3.pdb
***The runtime messages: [newhoir@localhost rubber]$ ./r 'import site' failed; use -v for traceback Traceback (most recent call last): File "mod-rubber1.py", line 18, in ? a.make() # do the actual homology modeling File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 424, in homcsr self.check_alignment(aln) File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 406, in check_alignment aln.check() File "/usr/lib/modeller9v8/modlib/modeller/alignment.py", line 200, in check self.check_structure_structure(io=io) File "/usr/lib/modeller9v8/modlib/modeller/alignment.py", line 209, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " A", chain " 3"; atom file name: /home/newhoir/rubber/atom_files/2d2r.pdb [newhoir@localhost rubber]$
***The file 2d2r.pdb is exactly as I downloaded it from RCSB
**The first lines of the header: HEADER TRANSFERASE 16-SEP-05 2D2R TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UNDECAPRENYL PYROPHOSPHATE TITLE 2 SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNDECAPRENYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B;
**The opening ATOM records: ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020149 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006518 0.00000 ATOM 1 N SER A 3 -4.458 53.857 94.802 1.00 59.58 N ATOM 2 CA SER A 3 -4.745 52.989 93.628 1.00 59.67 C ATOM 3 C SER A 3 -3.414 52.652 92.952 1.00 59.42 C ATOM 4 O SER A 3 -2.843 51.569 93.142 1.00 59.53 O