On Jun 16, 2025, at 1:56 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:Hi Sasha,_______________________________________________No web services are working right now, so this isn’t a problem specific to you. I’ll send mail once web services are working again.—EricOn Jun 16, 2025, at 7:44 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:_______________________________________________Hi All,I have run into difficulties when trying to model loops in ChimeraX. I have successfully aligned the structure with the FASTA sequence, but no matter which switch I use in the commandmodeller refine 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standardi.e., all-missing, internal-missing, or only a selected region, I get identical error:Opened 1 sequence from 7tdg.fasta
Associated 7tdi_orig_mod.pdb chain A to sp|7tdg_core with 0 mismatches and/or gaps
ui tool show "Model Loops"Exception in thread Thread-18 (_run_function):modeller refine 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\threading.py", line 1038, in _bootstrap_inner
self.run()
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\threading.py", line 975, in run
self._target(*self._args, **self._kwargs)
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-packages\chimerax\core\tasks.py", line 300, in _run_function
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-packages\chimerax\webservices\cxservices_job.py", line 156, in run
reason = json.loads(e.body)["description"]
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\json\__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\json\decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\json\decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Could you please let me know what the problem may be?Thanks!Sasha
From: Eric <pett@cgl.ucsf.edu>
To: Alexandra <alexandra.zahradnikova@savba.sk>
Cc: chimerax-users <chimerax-users@cgl.ucsf.edu>
Date: Tuesday, 1 April 2025 1:55 AM CEST
Subject: Re: [chimerax-users] Model loops with MODELER in ChimeraX
Hi again Sasha,You should be able to do this with a FASTA file and a PDB with the SEQRES records removed. This worked fine for me in a test situation where I had a structure with a missing segment and a FASTA sequence that corresponded except the missing part had been turned into alanines (more residues than the original missing segment). The fact that this doesn’t work for you suggests to me that the FASTA sequence you opened doesn’t match well to the existing parts of the structure. If you right click on the sequence and choose “Associations…” and then force the structure to associate with the sequence, do you get a lot of red error boxes on the sequence?You might have to open a ticket for this (Help→Report a Bug) and attach the sequence and structure files for me to offer further advice. If the data is private, you could email it to me directly.--EricEric PettersenUCSF Computer Graphics Lab
On Mar 28, 2025, at 7:54 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:_______________________________________________Hello,I have recently watched a Youtube video (https://www.youtube.com/watch?v=GV6jHhxR5T4) about completing loops with Modeller in ChimeraX. However, the structure I want to model is only a part of the actual molecule, and I want to replace one unresolved segment (300 residues long) with 11 glycines.When I upload both, the FASTA file with the sequence as it should look after completion of the loops, and the PDB file of the incomplete structure, I am not able to align them together in order to perform the modelling.- If I use the original PDB file containing the SEQRES part, the association is performed but produces mismatches after the start of the unresolved sequence.- If I use the PDB file without the SEQRES part, I am not able to perform the association.Can anybody help me?Thanks in advanceSasha________________________________________________________________________Alexandra Zahradníková, PhDDepartment of Cell CardiologyInstitute of Experimental EndocrinologyBiomedical Research Centre SASDúbravská cesta 9845 05 BratislavaSlovakiaMobile: +421 908 069 796
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/