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 > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >