Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 99, in
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py", line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 624, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 577, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 438 439 For alignment entry: 1 7B6W_proc.pdb_1
Another question: how could I use automatically the command
modeller refine 1/1:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard
which also does not work
This is all explained in the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html>
"The following are required for each chain to be modeled:
1. The atomic structure of at least part of the protein, open in ChimeraX.
2. A sequence that includes the segments to be filled in or refined [...] The target sequence can be taken from the structure metadata (and shown for a specific chain using the menu: Tools... Sequence... Show Sequence Viewer), or fetched from UniProt, or opened from a file.
3. A Modeller license key[...]"
However, if you give the license key once it should be remembered in your preferences and you don't have to give again. This also explained in the help.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/modeller.html#licenseKey>
Elaine
> On Mar 29, 2024, at 9:05 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
>
> Okay thank you very much Elaine !
>
> Actually I've tried it with the ChimeraX 1.6 so I will check it with the 1.7.1 version no problem.
>
> Also as I understood I need always to load fasta sequence (containing full sequence) from the separate file in the case if it's absent in the PDB, needn't it ?
>
> Does the command "modeller refine .." requires the licence key for the Modelled like it's in Gui ??
>
> And yes HAPPY HOLLIDAY ! 😀😃
>
> Yours with thanks
>
> Enrico
>
> Il giorno ven 29 mar 2024 alle ore 16:59 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
> Hi,
> I don't know why your specific case of modeling a missing loop from a protein in a complex didn't work. In general, it can work, e.g.
>
> open 4f88
> hide
> cartoon
> seq chain /1
> ui tool show "Model Loops"
> modeller refine 1/1:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard
>
> ... works fine for me in a recent daily build. The "modeller refine" command is just what I got from using the context menu in the sequence window (chain /1) to open Model Loops GUI and then clicking Apply with default options to fill in internal missing structure.
>
> It is probably something specific about your sequence and structure data, but when you get the error, you would need to use Help... Report a Bug and attach your session that contains this data, for us to be able to say why.
>
> Today is a work holiday for us so you may not get any more replies for a while.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Resource for Biocomputing, Visualization, and Informatics
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Mar 29, 2024, at 4:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
> >
> > Here is some update:
> > following the tutorial https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-modeling.html
> > I could do the trick but there are still some questions..
> >
> > First I loaded the structure with missed loop and the fasta file contained the full sequence and associate them together
> > open onlyB1Ar.pdb
> > open ./a.fasta
> > sequence associatee /A
> >
> > Then using the GUI I run modelled on server which produced 3 modells with missed loop. Everything is OK.
> >
> > Now I loaded the same structure (with missed loop) bound to another protein. Then I assosiated the fasta file to the chain A ( which is the structure with missed loop):
> > sequence associatee /A
> > Associated 6tko_proc.pdb chain A to 6TKO_1|Chain A|Beta-1 adrenergic receptor|Meleagris gallopavo (9103) with 0 mismatches and/or gaps
> >
> > Then I run modelled via the loop modeling GUI which produces the following error:
> >
> > Modeller failure; standard error:
> > Traceback (most recent call last):
> > File "ModellerModelling.py", line 93, in
> > a.make()
> > File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py", line 42, in make
> > AutoModel.make(self, exit_stage)
> > File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 141, in make
> > self.homcsr(exit_stage)
> > File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 624, in homcsr
> > self.check_alignment(aln)
> > File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 577, in check_alignment
> > aln.check()
> > File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in check
> > self.check_structure_structure(io=io)
> > File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in check_structure_structure
> > return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
> > _modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 624 280 For alignment entry: 1 6tko_proc.pdb_1
> >
> > I believe the problem could be related to the presence of the second protein in the complex (chain B) which however was not assosiated with the sequence from the fasta file.
> >
> > Consequently, every time to model a loop I need to extract the chain A from the complex, do the modeling and then combine it back with the chain B.
> > Is it possible to fix the issue in some way?
> >
> > Many thanks in advance !
> >
> > Enrico
> >
> > Il giorno ven 29 mar 2024 alle ore 10:00 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
> > Dear Chimera-X user!
> >
> > I am preparing a model of GPCR protein for the molecular dynamics simulation.
> > In this structure there is a loop fragment of 10-20 residues which is missed. Is it possible to reconstruct it (e.g. based on the sequence information or alternatively just add manually the missing fragment) using some tool of Chimera-X e.g. combining with the bond command ?
> >
> > Many thanks in advance !
> >
> > Enrico
>