Well, it's still saying that it can't find the alignment codes
read_al_230W> Alignment code alpha_tubulin is present multiple times in the
              alignment file! Only the first entry will be read.
              Suggest you remove the duplicate(s) to avoid confusion.
read_al_373E> Protein specified in ALIGN_CODES(i) was not found
              in the alignment file; ALIGN_CODES(       1) =  alpha_tubulin.pdb
Best,
Ajasja

On Thu, 10 May 2018 at 22:24, Ahmad Abdelzaher <underoath006@gmail.com> wrote:
I know this error usually happens when I get the names incorrectly. However, in this case, everything is fine and it seems to run for a little while, then it starts writing stuff to my .ali file and give the below error.  


readlinef__W> File: alpha_tubulin.pdb, Line: 4611
              Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4612
              Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4613
              Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4614
              Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4615
              Modeller will only read the first 80 characters of this line.

readlinef__W> File: alpha_tubulin.pdb, Line: 4616
              No more warnings will be printed for truncated lines in this file.

mkapsa__637W> No residue topology library is in memory.
              Better radii would be used if topology.read() is called first.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  N -->  N
              This message is written only for the first such atom.

Pairwise dynamic programming alignment (ALIGN2D):
  Residue-residue metric   : $(LIB)/as1.sim.mat
  Diagonal                 :          100
  Overhang                 :            0
  Maximal gap length       :       999999
  Local alignment          :            F
  MATRIX_OFFSET (local aln):       0.0000
  FIX_OFFSETS              :      0.0    -1.0    -2.0    -3.0    -4.0
  N_SUBOPT                 :            0
  SUBOPT_OFFSET            :       0.0000
  Alignment block          :            1
  Gap introduction penalty :    -100.0000
  Gap extension penalty    :       0.0000
  Gap diagonal penalty     :       0.0000
  Structure gap penalties  :    3.500   3.500   3.500   0.200   4.000   6.500   2.000   0.000
  Break-break bonus        :   10000.0000
  Length of alignment      :          441
  Score                    :  258659.2969
read_al_230W> Alignment code alpha_tubulin is present multiple times in the
              alignment file! Only the first entry will be read.
              Suggest you remove the duplicate(s) to avoid confusion.
read_al_373E> Protein specified in ALIGN_CODES(i) was not found
              in the alignment file; ALIGN_CODES(       1) =  alpha_tubulin.pdb
Traceback (most recent call last):

  File "<ipython-input-12-d935bbc074eb>", line 1, in <module>
    runfile('/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller/modeller.py', wdir='/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller')

  File "/home/labusr/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 714, in runfile
    execfile(filename, namespace)

  File "/home/labusr/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 89, in execfile
    exec(compile(f.read(), filename, 'exec'), namespace)

  File "/home/labusr/Desktop/chlamy_paper/denovo_prediction/alpha_tubulin/Modeller/modeller.py", line 35, in <module>
    a.make()

  File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 112, in make
    self.homcsr(exit_stage)

  File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 535, in homcsr
    aln = self.read_alignment()

  File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/automodel/automodel.py", line 502, in read_alignment
    aln.append(file=self.alnfile, align_codes=codes)

  File "/home/labusr/anaconda3/lib/python3.5/site-packages/modeller/alignment.py", line 80, in append
    allow_alternates)

ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(       1) =  alpha_tubulin.pdb
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