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