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