Model loops with MODELER in ChimeraX
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 advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796
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. --Eric Eric Pettersen UCSF 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 advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Eric, Thanks for the suggestion. I found out that the problem was that I was trying to associate the FASTA sequence and the structure sequence from the sequence viewer, not from the FASTA sequence. Now it works, no errors! Best Sasha -----Original Message----- 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. --Eric Eric Pettersen UCSF 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 advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796 _______________________________________________ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.eduTo unsubscribe send an email to chimerax-users-leave@cgl.ucsf.eduArchives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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 command modeller refine 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard i.e., all-missing, internal-missing, or only a selected region, I get identical error: Opened 1 sequence from 7tdg.fasta sequence associate /A Associated 7tdi_orig_mod.pdb chain A to sp|7tdg_core with 0 mismatches and/or gaps ui tool show "Model Loops" modeller refine 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard Exception in thread Thread-18 (_run_function): 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 -----Original Message----- 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. --Eric Eric Pettersen UCSF 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 advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796 _______________________________________________ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.eduTo unsubscribe send an email to chimerax-users-leave@cgl.ucsf.eduArchives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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. —Eric
On 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 command modeller refine <help:user/commands/modeller.html#refine> 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard i.e., all-missing, internal-missing, or only a selected region, I get identical error:
Opened 1 sequence from 7tdg.fasta sequence associate <help:user/commands/sequence.html#associate> /A Associated 7tdi_orig_mod.pdb chain A to sp|7tdg_core with 0 mismatches and/or gaps ui tool show <help:user/commands/ui.html#tool-show> "Model Loops" modeller refine <help:user/commands/modeller.html#refine> 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard Exception in thread Thread-18 (_run_function): 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.
--Eric
Eric Pettersen UCSF 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 advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto: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/
Hi Sasha, Web services are working again, so please try your Modeller job again. —Eric
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.
—Eric
On 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 command modeller refine <help:user/commands/modeller.html#refine> 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard i.e., all-missing, internal-missing, or only a selected region, I get identical error:
Opened 1 sequence from 7tdg.fasta sequence associate <help:user/commands/sequence.html#associate> /A Associated 7tdi_orig_mod.pdb chain A to sp|7tdg_core with 0 mismatches and/or gaps ui tool show <help:user/commands/ui.html#tool-show> "Model Loops" modeller refine <help:user/commands/modeller.html#refine> 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard Exception in thread Thread-18 (_run_function): 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.
--Eric
Eric Pettersen UCSF 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 advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto: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/
Thanks!!! SashaSent from my Galaxy -------- Original message --------From: Eric Pettersen <pett@cgl.ucsf.edu> Date: 16/06/2025 23:41 (GMT+01:00) To: Alexandra Zahradnikova <http://Alexandra.Zahradnikova@savba.sk> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Model loops with MODELER in ChimeraX Hi Sasha, Web services are working again, so please try your Modeller job again.—EricOn 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 command modeller refine 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard i.e., all-missing, internal-missing, or only a selected region, I get identical error: Opened 1 sequence from 7tdg.fasta sequence associate /A Associated 7tdi_orig_mod.pdb chain A to sp|7tdg_core with 0 mismatches and/or gaps ui tool show "Model Loops" modeller refine 7tdg.fasta:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard Exception in thread Thread-18 (_run_function):Traceback (most recent call last):File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\threading.py", line 1038, in _bootstrap_innerself.run()File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\threading.py", line 975, in runself._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_functionfunc(*args, **kw)File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-packages\chimerax\webservices\cxservices_job.py", line 156, in runreason = json.loads(e.body)["description"]^^^^^^^^^^^^^^^^^^File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\json\__init__.py", line 346, in loadsreturn _default_decoder.decode(s)^^^^^^^^^^^^^^^^^^^^^^^^^^File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\json\decoder.py", line 337, in decodeobj, 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_decoderaise JSONDecodeError("Expecting value", s, err.value) from Nonejson.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 <http://alexandra.zahradnikova@savba.sk>Cc: chimerax-users <chimerax-users@cgl.ucsf.edu>Date: Tuesday, 1 April 2025 1:55 AM CESTSubject: Re: [chimerax-users] Model loops with MODELER in ChimeraXHi 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. --Eric Eric Pettersen UCSF 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 advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796 _______________________________________________ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.eduTo unsubscribe send an email to chimerax-users-leave@cgl.ucsf.eduArchives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ _______________________________________________ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.eduTo unsubscribe send an email to chimerax-users-leave@cgl.ucsf.eduArchives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... mailing list -- chimerax-users@cgl.ucsf.eduTo unsubscribe send an email to chimerax-users-leave@cgl.ucsf.eduArchives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
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Alexandra Zahradnikova -
Alexandra Zahradnikova
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Eric Pettersen