Fwd: Error in modeller 10.5
---------- Forwarded message --------- De: Victor Eduardo Rojas Pérez victor.rojas.03@alu.ucm.cl Date: mar, 3 sept 2024 a las 13:11 Subject: Error in modeller 10.5 To: Modeller Caretaker modeller-care@salilab.org, < modeller_usage@salilab.org>
Dear All,
Along with greeting them cordially. I have the following error using modeller 10.5. in linux operating system. I have added the restyp RTN, retinal with % symbol in the restyp.lib file in the modlib folder but I still have this error. What else could I do to solve this error.
Thank you.
mod10.5 align1.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "align1.py", line 56, in ? a.make() # do homology modeling File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 611, in homcsr aln = self.read_alignment() File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 572, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File "/usr/lib/modeller10.5/modlib/modeller/alignment.py", line 82, in append allow_alternates) _modeller.ModellerError: read_al_375E> Unknown residue type,position,sequence: % 334 1
On 9/3/24 10:24 AM, Victor Eduardo Rojas Pérez wrote: > I have the following error using modeller 10.5. in linux operating > system. I have added the restyp RTN, retinal with % symbol in the > restyp.lib file in the modlib folder but I still have this error. > What else could I do to solve this error. ... > _modeller.ModellerError: read_al_375E> Unknown residue > type,position,sequence: % 334 1
This indicates that either you did not edit the file correctly, or you edited the wrong file (in your case, it looks like the file you need to edit is /usr/lib/modeller10.5/modlib/restyp.lib).
If all you want to do is copy one or more retinal residues from your template structure to your target model, the easiest way to do that is to simply use the '.' residue in your alignment file; see https://salilab.org/modeller/10.5/manual/node18.html
If you want to model the residue(s) flexibly, you can certainly do that but the procedure can be quite involved: https://salilab.org/modeller/FAQ.html#8
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Victor Eduardo Rojas Pérez