Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5524 closed defect (fixed)

Modeller failure

Reported by: dstnt@… Owned by: pett
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
While generating the models, 4 out of 5 models had been generated, but then the procedure crashed with the error message

chimerax.core.tasks.JobError: Server raised fault: ''

File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\webservices\opal_job.py", line 300, in get_outputs
raise JobError(str(e))

See log for complete Python traceback.

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\labuser\Downloads\rcsb_pdb_1MW8.fasta format fasta alignment
> false

Summary of feedback from opening
C:\Users\labuser\Downloads\rcsb_pdb_1MW8.fasta  
---  
notes | Alignment identifier is rcsb_pdb_1MW8.fasta-1  
Alignment identifier is rcsb_pdb_1MW8.fasta-2  
  
Opened 2 sequences from rcsb_pdb_1MW8.fasta  

> ui tool show "Modeller Comparative"

> open C:\Users\labuser\Downloads\rcsb_pdb_1MW8.fasta format fasta alignment
> false

Summary of feedback from opening
C:\Users\labuser\Downloads\rcsb_pdb_1MW8.fasta  
---  
notes | Destroying pre-existing alignment with identifier
rcsb_pdb_1MW8.fasta-1  
Alignment identifier is rcsb_pdb_1MW8.fasta-1  
Destroying pre-existing alignment with identifier rcsb_pdb_1MW8.fasta-2  
Alignment identifier is rcsb_pdb_1MW8.fasta-2  
  
Opened 2 sequences from rcsb_pdb_1MW8.fasta  

> open 2bbv format mmcif fromDatabase pdb

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description  
A B C | protein (black beetle virus capsid protein)  
D E F | protein (black beetle virus capsid protein)  
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3')  
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> close

> ui tool show "File History"

> ui tool show Log

> ui tool show "Blast Protein"

> open C:\Users\labuser\Downloads\rcsb_pdb_1MW8.fasta format fasta alignment
> false

Summary of feedback from opening
C:\Users\labuser\Downloads\rcsb_pdb_1MW8.fasta  
---  
notes | Alignment identifier is rcsb_pdb_1MW8.fasta-1  
Alignment identifier is rcsb_pdb_1MW8.fasta-2  
  
Opened 2 sequences from rcsb_pdb_1MW8.fasta  

> open C:\ProgramData\ChimeraX\4rul_chimerax_modeller4.pdb format pdb

Summary of feedback from opening
C:\ProgramData\ChimeraX\4rul_chimerax_modeller4.pdb  
---  
warning | Ignored bad PDB record found on line 6762  
END  
  
Chain information for 4rul_chimerax_modeller4.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Blast Protein"

> open pdb:4RUL format mmcif fromDatabase pdb

4rul title:  
Crystal structure of full-length E.Coli topoisomerase I in complex with ssDNA
[more info...]  
  
Chain information for 4rul #2  
---  
Chain | Description  
A | DNA topoisomerase 1  
B | single strand DNA  
  
Non-standard residues in 4rul #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
SO4 — sulfate ion  
ZN — zinc ion  
  
Associated 4rul chain A to 1MW8_2|Chain B[auth X]|DNA Topoisomerase
I|Escherichia coli (562) with 3 mismatches  

> ui tool show "Model Panel"

> hide #1 models

> ui tool show "Modeller Comparative"

> modeller comparative rcsb_pdb_1MW8.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false waterPreserve false

Alignment rcsb_pdb_1MW8.fasta-1 has no associated chains  

> hide #!2 models

> show #1 models

> hide #1 models

> close #1

> select /A:5

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:5-319

2242 atoms, 2287 bonds, 1 pseudobond, 294 residues, 2 models selected  

> select /A:2-320

2265 atoms, 2310 bonds, 1 pseudobond, 298 residues, 2 models selected  

> select /A:592

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2-592

4366 atoms, 4453 bonds, 2 pseudobonds, 567 residues, 2 models selected  

> ui tool show "Modeller Comparative"

> modeller comparative rcsb_pdb_1MW8.fasta-2:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1635866031613-1821751779  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1635866031613-1821751779  
stdout.txt = standard output  
stderr.txt = standard error  

> ui tool show "Modeller Comparative"

> modeller comparative rcsb_pdb_1MW8.fasta-2:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1635866047511854391850  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1635866047511854391850  
stdout.txt = standard output  
stderr.txt = standard error  

> ui tool show Log

> close

> ui windowfill toggle

> ui windowfill toggle

> ui tool show "Modeller Comparative"

<suds.sax.document.Document object at 0x0000025381093A00>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 82, in send  
fp = self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 640, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 569, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 502, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 500: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 613, in send  
reply = self.options.transport.send(request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\https.py", line 66, in send  
return HttpTransport.send(self, request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 94, in send  
raise TransportError(e.msg, e.code, e.fp)  
suds.transport.TransportError: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 297, in get_outputs  
r = self._suds.service.getOutputs(self.job_id)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 521, in __call__  
return client.invoke(args, kwargs)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 581, in invoke  
result = self.send(soapenv)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 618, in send  
return self.process_reply(reply=content, status=e.httpcode,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 670, in process_reply  
raise WebFault(fault, replyroot)  
suds.WebFault: Server raised fault: ''  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tasks.py", line 288, in run  
self.monitor()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 428, in monitor  
stdout = self.get_file("stdout.txt")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 262, in get_file  
self.get_outputs()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
Exception in thread 1:  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
  
See log for complete Python traceback.  
  
Modeller job ID appModeller9v8Service1635866031613-1821751779 finished  
<suds.sax.document.Document object at 0x000002538061ABB0>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 82, in send  
fp = self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 640, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 569, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 502, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 500: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 613, in send  
reply = self.options.transport.send(request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\https.py", line 66, in send  
return HttpTransport.send(self, request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 94, in send  
raise TransportError(e.msg, e.code, e.fp)  
suds.transport.TransportError: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 297, in get_outputs  
r = self._suds.service.getOutputs(self.job_id)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 521, in __call__  
return client.invoke(args, kwargs)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 581, in invoke  
result = self.send(soapenv)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 618, in send  
return self.process_reply(reply=content, status=e.httpcode,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 670, in process_reply  
raise WebFault(fault, replyroot)  
suds.WebFault: Server raised fault: ''  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 453, in on_finish  
model_info = self.get_file("ok_models.dat")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 262, in get_file  
self.get_outputs()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
  
See log for complete Python traceback.  
  
<suds.sax.document.Document object at 0x000002538078DDF0>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 82, in send  
fp = self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 640, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 569, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 502, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 500: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 613, in send  
reply = self.options.transport.send(request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\https.py", line 66, in send  
return HttpTransport.send(self, request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 94, in send  
raise TransportError(e.msg, e.code, e.fp)  
suds.transport.TransportError: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 297, in get_outputs  
r = self._suds.service.getOutputs(self.job_id)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 521, in __call__  
return client.invoke(args, kwargs)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 581, in invoke  
result = self.send(soapenv)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 618, in send  
return self.process_reply(reply=content, status=e.httpcode,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 670, in process_reply  
raise WebFault(fault, replyroot)  
suds.WebFault: Server raised fault: ''  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tasks.py", line 288, in run  
self.monitor()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 428, in monitor  
stdout = self.get_file("stdout.txt")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 262, in get_file  
self.get_outputs()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
Exception in thread 2:  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
  
See log for complete Python traceback.  
  
Modeller job ID appModeller9v8Service1635866047511854391850 finished  
<suds.sax.document.Document object at 0x000002538061A5E0>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 82, in send  
fp = self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 640, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 569, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 502, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 500: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 613, in send  
reply = self.options.transport.send(request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\https.py", line 66, in send  
return HttpTransport.send(self, request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 94, in send  
raise TransportError(e.msg, e.code, e.fp)  
suds.transport.TransportError: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 297, in get_outputs  
r = self._suds.service.getOutputs(self.job_id)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 521, in __call__  
return client.invoke(args, kwargs)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 581, in invoke  
result = self.send(soapenv)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 618, in send  
return self.process_reply(reply=content, status=e.httpcode,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 670, in process_reply  
raise WebFault(fault, replyroot)  
suds.WebFault: Server raised fault: ''  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 453, in on_finish  
model_info = self.get_file("ok_models.dat")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 262, in get_file  
self.get_outputs()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
  
See log for complete Python traceback.  
  

> close #

Expected a models specifier or a keyword  

> open C:/Users/labuser/Downloads/rcsb_pdb_4RUL.fasta

Sequence '4RUL_2|Chain B|single strand DNA|synthetic construct (32630)'
differs in length from preceding sequences, and it is therefore impossible to
open these sequences as an alignment. If you want to open the sequences
individually, specify 'false' as the value of the 'alignment' keyword in the
'open' command.  

> open C:/Users/labuser/Downloads/rcsb_pdb_4RUL.fasta alignment false

Summary of feedback from opening
C:/Users/labuser/Downloads/rcsb_pdb_4RUL.fasta  
---  
notes | Alignment identifier is rcsb_pdb_4RUL.fasta-1  
Alignment identifier is rcsb_pdb_4RUL.fasta-2  
  
Opened 2 sequences from rcsb_pdb_4RUL.fasta  

> ui tool show "Modeller Comparative"

> modeller comparative rcsb_pdb_4RUL.fasta-1:1 rcsb_pdb_4RUL.fasta-2:1
> multichain true numModels 5 fast false hetPreserve false hydrogens false
> waterPreserve false

Alignment rcsb_pdb_4RUL.fasta-1 has no associated chains  

> modeller comparative rcsb_pdb_4RUL.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false waterPreserve false

Alignment rcsb_pdb_4RUL.fasta-1 has no associated chains  

> blastprotein rcsb_pdb_4RUL.fasta-1:1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1635866382806-767115372  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1635866382806-767115372  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

> ui tool show "Modeller Comparative"

Alignment identifier is bp3 [1]  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp3 [1]  

> modeller comparative "bp3 [1]:2" multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Alignment bp3 [1] has no associated chains  

> modeller comparative "bp3 [1]:1" multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Alignment bp3 [1] has no associated chains  

> open C:\Users\labuser\Downloads\rcsb_pdb_4RUL.fasta format fasta alignment
> false

Summary of feedback from opening
C:\Users\labuser\Downloads\rcsb_pdb_4RUL.fasta  
---  
notes | Alignment identifier is rcsb_pdb_4RUL.fasta-1  
Alignment identifier is rcsb_pdb_4RUL.fasta-2  
  
Opened 2 sequences from rcsb_pdb_4RUL.fasta  

> open pdb:4RUL format mmcif fromDatabase pdb

4rul title:  
Crystal structure of full-length E.Coli topoisomerase I in complex with ssDNA
[more info...]  
  
Chain information for 4rul #1  
---  
Chain | Description  
A | DNA topoisomerase 1  
B | single strand DNA  
  
Non-standard residues in 4rul #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
SO4 — sulfate ion  
ZN — zinc ion  
  
Associated 4rul chain A to 4RUL_1|Chain A|DNA topoisomerase 1|Escherichia coli
DH1 (536056) with 0 mismatches  
Associated 4rul chain B to 4RUL_2|Chain B|single strand DNA|synthetic
construct (32630) with 0 mismatches  

> select sequence 4RUL.pdb

Nothing selected  

> modeller comparative rcsb_pdb_4RUL.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false tempPath
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1635866594841-1157084970  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1635866594841-1157084970  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1635866594841-1157084970 finished  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4rul, chain A (#1) with 4RUL_1_Chain_A_D, chain A (#), sequence
alignment score = 4255.2  
RMSD between 606 pruned atom pairs is 0.472 angstroms; (across all 821 pairs:
2.951)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4rul, chain A (#1) with 4RUL_1_Chain_A_D, chain A (#), sequence
alignment score = 4247.4  
RMSD between 691 pruned atom pairs is 0.681 angstroms; (across all 821 pairs:
2.090)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4rul, chain A (#1) with 4RUL_1_Chain_A_D, chain A (#), sequence
alignment score = 4261.2  
RMSD between 652 pruned atom pairs is 0.672 angstroms; (across all 821 pairs:
2.596)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4rul, chain A (#1) with 4RUL_1_Chain_A_D, chain A (#), sequence
alignment score = 4267.8  
RMSD between 629 pruned atom pairs is 0.652 angstroms; (across all 821 pairs:
2.578)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4rul, chain A (#1) with 4RUL_1_Chain_A_D, chain A (#), sequence
alignment score = 4272.6  
RMSD between 707 pruned atom pairs is 0.711 angstroms; (across all 821 pairs:
1.855)  
  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Chain information for 4RUL_1_Chain_A_D  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A | No description available  
  

> hide #!1 models

> hide #!2 models

> hide #2.1 models

> hide #2.2 models

> hide #2.3 models

> hide #2.4 models

> hide #2.5 models

> show #2.1 models

> show #!1 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> open C:\ProgramData\ChimeraX\4rul_chimerax_modeller3.pdb format pdb

Chain information for 4rul_chimerax_modeller3.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

> hide #1.1 models

> hide #1.2 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> modeller scores #2.1-5 refresh false

> hide #!2 models

> hide #2.1 models

> hide #2.2 models

> show #2.1 models

> hide #2.3 models

> hide #2.4 models

> hide #2.5 models

> ui tool show "Modeller Comparative"

> ui tool show "Show Sequence Viewer"

> hide #2.1 models

> show #2.1 models

> show #!1 models

> show #2.2 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #1.2 models

> hide #1.2 models

> hide #!2 models

> hide #2.2 models

> hide #!1 models

> open C:/Users/labuser/Downloads/rcsb_pdb_4RUL.fasta

Sequence '4RUL_2|Chain B|single strand DNA|synthetic construct (32630)'
differs in length from preceding sequences, and it is therefore impossible to
open these sequences as an alignment. If you want to open the sequences
individually, specify 'false' as the value of the 'alignment' keyword in the
'open' command.  

> open C:/Users/labuser/Downloads/rcsb_pdb_4RUL.fasta alignment false

Summary of feedback from opening
C:/Users/labuser/Downloads/rcsb_pdb_4RUL.fasta  
---  
notes | Alignment identifier is rcsb_pdb_4RUL.fasta-1  
Associated 4rul chain A to 4RUL_1|Chain A|DNA topoisomerase 1|Escherichia coli
DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D (2.1) chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D (2.2) chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D (2.3) chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D (2.4) chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
1 messages similar to the above omitted  
Alignment identifier is rcsb_pdb_4RUL.fasta-2  
Associated 4rul chain B to 4RUL_2|Chain B|single strand DNA|synthetic
construct (32630) with 0 mismatches  
  
Opened 2 sequences from rcsb_pdb_4RUL.fasta  

> ui tool show "Modeller Comparative"

> modeller comparative rcsb_pdb_4RUL.fasta-1:1 rcsb_pdb_4RUL.fasta-2:1
> multichain true numModels 5 fast false hetPreserve false hydrogens false
> tempPath C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service163586718845839926187  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service163586718845839926187  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service163586718845839926187 finished  
  
Modeller error output  
Traceback (most recent call last):  
File "/usr/local/opal-local/bin/modeller9v8.py", line 332, in <module>  
main()  
File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main  
VersionMap[cf["version"]](cf)  
File "/usr/local/opal-local/bin/modeller9v8.py", line 34, in v2_run  
execfile(fn)  
File "ModellerModelling.py", line 67, in <module>  
a.make()  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 141, in make  
self.homcsr(exit_stage)  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 612, in homcsr  
aln = self.read_alignment()  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 573, in read_alignment  
aln.append(file=self.alnfile, align_codes=codes)  
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 82, in
append  
allow_alternates)  
_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not
match that in PDB file: 1 ./4rul_1.pdb (You didn't specify the starting and
ending residue numbers and chain IDs in the alignment, so Modeller tried to
guess these from the PDB file.) Suggestion: put in the residue numbers and
chain IDs (see the manual) and run again for more detailed diagnostics. You
could also try running with allow_alternates=True to accept alternate one-
letter code matches (e.g. B to N, Z to Q).  
  
  
Modeller run output  
**** IGNORE FOLLOWING LICENSE KEY MESSAGE ****  
check_lice_E> Invalid license key: xxx  
Go to https://salilab.org/modeller/ to get a license key,  
and then set the 'license' variable to it in the file  
/usr/lib/modeller10.1/modlib/modeller/config.py  
  
**** END IGNORED MESSAGE ****  
  
MODELLER 10.1, 2021/03/12, r12156  
  
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS  
  
  
Copyright(c) 1989-2021 Andrej Sali  
All Rights Reserved  
  
Written by A. Sali  
with help from  
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,  
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,  
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,  
F. Melo, J.P. Overington, E. Feyfant  
University of California, San Francisco, USA  
Rockefeller University, New York, USA  
Harvard University, Cambridge, USA  
Imperial Cancer Research Fund, London, UK  
Birkbeck College, University of London, London, UK  
  
  
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
3.10.0-1160.36.2.el7.x86_64 x86_64  
Date and time of compilation : 2021/03/12 00:18:43  
MODELLER executable type : x86_64-intel8  
Job starting time (YY/MM/DD HH:MM:SS): 2021/11/02 08:33:08  
  
environ____W> The class 'environ' is deprecated; use 'Environ' instead  
openf___224_> Open $(LIB)/restyp.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/resgrp.lib  
rdresgr_266_> Number of residue groups: 2  
openf___224_> Open ${MODINSTALL10v1}/modlib/sstruc.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183  
openf___224_> Open ${MODINSTALL10v1}/modlib/resdih.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230  
rdrdih__263_> Number of dihedral angle types : 9  
Maximal number of dihedral angle optima: 3  
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5  
openf___224_> Open ${MODINSTALL10v1}/modlib/radii.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242  
openf___224_> Open ${MODINSTALL10v1}/modlib/af_mnchdef.lib  
rdwilmo_274_> Mainchain residue conformation classes: APBLE  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch.lib  
rdclass_257_> Number of classes: 5  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch1.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch2.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch3.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/xs4.mat  
rdrrwgh_268_> Number of residue types: 21  
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead  
openf___224_> Open alignment.ali  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 285310 278.623
0.272  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 302607 295.515
0.289  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 320257 312.751
0.305  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 355557 347.224
0.339  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 426157 416.169
0.406  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 567357 554.060
0.541  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 849757 829.841
0.810  
openf___224_> Open ./4rul_1.pdb  
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./4rul_1.pdb  
(You didn't specify the starting and ending residue numbers and  
chain IDs in the alignment, so Modeller tried to guess these from  
the PDB file.)  
Suggestion: put in the residue numbers and chain IDs (see the  
manual) and run again for more detailed diagnostics.  
You could also try running with allow_alternates=True to accept  
alternate one-letter code matches (e.g. B to N, Z to Q).  
  
Alignment sequence:  
GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELK  
QLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMD  
RVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFR  
PVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRT  
DSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVA  
CQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPA  
RFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSL  
DQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYALP  
PKERCKTTINLVPENEVLNVLEGEDAETNALRAKRRCPKCGTAMDSYLIDPKRKLHVCGNNPTCDGYEIEEGEFR  
IKGYDGPIVECEKCGSEMHLKMGRFGKYMACTNEECKNTRKILRNGEVAPPKEDPVPLPELPCEKSDAYFVLRDG  
AAGVFLAANTFPKSRETRAPLVEEFRDRLPEKLRYLADAPNKTMVRFSRKTKQQYVSSEKGWSAFYVDGKWVETA  
TGCGATTTGGG  
  
PDB sequence matching range provided in alignment:  
GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELK  
QLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMD  
RVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFR  
PVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRT  
DSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVA  
CQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPA  
RFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSL  
DQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYALP  
PKERCKTTINLVPENEVLNVLEGEDAETNALRAKRRCPKCGTAMDSYLIDPKRKLHVCGNNPTCDGYEIEEGEFR  
IKGYDGPIVECEKCGSEMHLKMGRFGKYMACTNEECKNTRKILRNGEVAPPKEDPVPLPELPCEKSDAYFVLRDG  
AAGVFLAANTFPKSRETRAPLVEEFRDRLPEKLRYLADAPNKTMVRFSRKTKQQYVSSEKGWSAFYVDGKWVEte  
tljletttlll  
  
No output models from Modeller; see log for Modeller text output.  

> ui tool show "Modeller Comparative"

> modeller comparative rcsb_pdb_4RUL.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false tempPath
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1635867233334-636788509  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1635867233334-636788509  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1635867233334-636788509 finished  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4RUL_1_Chain_A_D, chain A (#2.1) with 4RUL_1_Chain_A_D, chain A
(#), sequence alignment score = 4429.2  
RMSD between 705 pruned atom pairs is 0.504 angstroms; (across all 867 pairs:
1.976)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4RUL_1_Chain_A_D, chain A (#2.1) with 4RUL_1_Chain_A_D, chain A
(#), sequence alignment score = 4412.4  
RMSD between 682 pruned atom pairs is 0.654 angstroms; (across all 867 pairs:
4.986)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4RUL_1_Chain_A_D, chain A (#2.1) with 4RUL_1_Chain_A_D, chain A
(#), sequence alignment score = 4425  
RMSD between 741 pruned atom pairs is 0.633 angstroms; (across all 867 pairs:
1.853)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4RUL_1_Chain_A_D, chain A (#2.1) with 4RUL_1_Chain_A_D, chain A
(#), sequence alignment score = 4402.2  
RMSD between 598 pruned atom pairs is 0.609 angstroms; (across all 867 pairs:
4.728)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4RUL_1_Chain_A_D, chain A (#2.1) with 4RUL_1_Chain_A_D, chain A
(#), sequence alignment score = 4410.6  
RMSD between 692 pruned atom pairs is 0.562 angstroms; (across all 867 pairs:
3.970)  
  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Associated 4RUL_1_Chain_A_D chain A to 4RUL_1|Chain A|DNA topoisomerase
1|Escherichia coli DH1 (536056) with 0 mismatches  
Chain information for 4RUL_1_Chain_A_D  
---  
Chain | Description  
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A | No description available  
  

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> hide #4.4 models

> hide #4.5 models

> hide #4.3 models

> show #4.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> modeller scores #4.1-5 refresh false

> help help:user/tools/modeller.html#output

> save
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models/4RUL_models_modeller.cxs

> save 4rul_chimerax_modeller_110221_1.pdb #4.1

> save 4rul_chimerax_modeller_110221_2.pdb #4.2

> save 4rul_chimerax_modeller_110221_3.pdb #4.3

> save 4rul_chimerax_modeller_110221_4.pdb #4.4

> save 4rul_chimerax_modeller_110221_5.pdb #4.5

> open C:/Users/labuser/Downloads/rcsb_pdb_1MW8.fasta

Sequence '1MW8_2|Chain B[auth X]|DNA Topoisomerase I|Escherichia coli (562)'
differs in length from preceding sequences, and it is therefore impossible to
open these sequences as an alignment. If you want to open the sequences
individually, specify 'false' as the value of the 'alignment' keyword in the
'open' command.  

> open C:/Users/labuser/Downloads/rcsb_pdb_1MW8.fasta alignment false

Summary of feedback from opening
C:/Users/labuser/Downloads/rcsb_pdb_1MW8.fasta  
---  
notes | Alignment identifier is rcsb_pdb_1MW8.fasta-1  
Alignment identifier is rcsb_pdb_1MW8.fasta-2  
Associated 4rul chain A to 1MW8_2|Chain B[auth X]|DNA Topoisomerase
I|Escherichia coli (562) with 3 mismatches  
Associated 4RUL_1_Chain_A_D (2.1) chain A to 1MW8_2|Chain B[auth X]|DNA
Topoisomerase I|Escherichia coli (562) with 3 mismatches  
Associated 4RUL_1_Chain_A_D (2.2) chain A to 1MW8_2|Chain B[auth X]|DNA
Topoisomerase I|Escherichia coli (562) with 3 mismatches  
Associated 4RUL_1_Chain_A_D (2.3) chain A to 1MW8_2|Chain B[auth X]|DNA
Topoisomerase I|Escherichia coli (562) with 3 mismatches  
Associated 4RUL_1_Chain_A_D (2.4) chain A to 1MW8_2|Chain B[auth X]|DNA
Topoisomerase I|Escherichia coli (562) with 3 mismatches  
6 messages similar to the above omitted  
  
Opened 2 sequences from rcsb_pdb_1MW8.fasta  

> ui tool show "Modeller Comparative"

> modeller comparative rcsb_pdb_1MW8.fasta-1:1 rcsb_pdb_1MW8.fasta-2:1
> multichain true numModels 5 fast false hetPreserve false hydrogens false
> tempPath C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Alignment rcsb_pdb_1MW8.fasta-1 has no associated chains  

> modeller comparative rcsb_pdb_1MW8.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false tempPath
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Alignment rcsb_pdb_1MW8.fasta-1 has no associated chains  

> select #1/A:26-39 #2.1/A:28-52 #2.2/A:28-52 #2.3/A:28-52 #2.4/A:28-52
> #2.5/A:28-52 #4.1/A:28-52 #4.2/A:28-52 #4.3/A:28-52 #4.4/A:28-52
> #4.5/A:28-52

1845 atoms, 1856 bonds, 264 residues, 11 models selected  

> select #1/A:26-250 #2.1/A:28-252 #2.2/A:28-252 #2.3/A:28-252 #2.4/A:28-252
> #2.5/A:28-252 #4.1/A:28-252 #4.2/A:28-252 #4.3/A:28-252 #4.4/A:28-252
> #4.5/A:28-252

19363 atoms, 19746 bonds, 1 pseudobond, 2454 residues, 12 models selected  
Seqview [ID: rcsb_pdb_1MW8.fasta-2] region 1MW8_2|Chain B[auth X]|DNA
Topoisomerase I|Escherichia coli (562) [26-250] RMSD: 1.816  
  

> select #1/A:2-25 #2.1/A:3-27 #2.2/A:3-27 #2.3/A:3-27 #2.4/A:3-27 #2.5/A:3-27
> #4.1/A:3-27 #4.2/A:3-27 #4.3/A:3-27 #4.4/A:3-27 #4.5/A:3-27

2027 atoms, 2049 bonds, 274 residues, 11 models selected  

> select #1/A:2-592 #2.1/A:3-594 #2.2/A:3-594 #2.3/A:3-594 #2.4/A:3-594
> #2.5/A:3-594 #4.1/A:3-594 #4.2/A:3-594 #4.3/A:3-594 #4.4/A:3-594
> #4.5/A:3-594

51316 atoms, 52303 bonds, 2 pseudobonds, 6487 residues, 12 models selected  
Seqview [ID: rcsb_pdb_1MW8.fasta-2] region 1MW8_2|Chain B[auth X]|DNA
Topoisomerase I|Escherichia coli (562) [1-592] RMSD: 1.311  
  

> modeller comparative rcsb_pdb_1MW8.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false tempPath
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Alignment rcsb_pdb_1MW8.fasta-1 has no associated chains  

> select #1.1

13 pseudobonds, 1 model selected  

> ~select #1.1

Nothing selected  

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> hide #4.3 models

> hide #4.4 models

> hide #4.5 models

> hide #!2 models

> modeller comparative rcsb_pdb_1MW8.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false tempPath
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Alignment rcsb_pdb_1MW8.fasta-1 has no associated chains  

> modeller comparative rcsb_pdb_1MW8.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false tempPath
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Alignment rcsb_pdb_1MW8.fasta-1 has no associated chains  

> modeller comparative rcsb_pdb_1MW8.fasta-1:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false tempPath
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Alignment rcsb_pdb_1MW8.fasta-1 has no associated chains  

> modeller comparative rcsb_pdb_1MW8.fasta-2:1 multichain true numModels 5
> fast false hetPreserve false hydrogens false tempPath
> C:/Users/labuser/Documents/Structure_predictions/ChimeraX_models
> waterPreserve false

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1635870491733-1823643232  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1635870491733-1823643232  
stdout.txt = standard output  
stderr.txt = standard error  
<suds.sax.document.Document object at 0x00000254325C85E0>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 82, in send  
fp = self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 640, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 569, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 502, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 500: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 613, in send  
reply = self.options.transport.send(request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\https.py", line 66, in send  
return HttpTransport.send(self, request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 94, in send  
raise TransportError(e.msg, e.code, e.fp)  
suds.transport.TransportError: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 297, in get_outputs  
r = self._suds.service.getOutputs(self.job_id)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 521, in __call__  
return client.invoke(args, kwargs)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 581, in invoke  
result = self.send(soapenv)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 618, in send  
return self.process_reply(reply=content, status=e.httpcode,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 670, in process_reply  
raise WebFault(fault, replyroot)  
suds.WebFault: Server raised fault: ''  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\tasks.py", line 288, in run  
self.monitor()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 428, in monitor  
stdout = self.get_file("stdout.txt")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 262, in get_file  
self.get_outputs()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
Exception in thread 17:  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
  
See log for complete Python traceback.  
  
Modeller job ID appModeller9v8Service1635870491733-1823643232 finished  
<suds.sax.document.Document object at 0x0000025432480070>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 82, in send  
fp = self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 640, in
http_response  
response = self.parent.error(  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 569, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 502, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\urllib\request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 500: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 613, in send  
reply = self.options.transport.send(request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\https.py", line 66, in send  
return HttpTransport.send(self, request)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\suds\transport\http.py", line 94, in send  
raise TransportError(e.msg, e.code, e.fp)  
suds.transport.TransportError: Internal Server Error  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 297, in get_outputs  
r = self._suds.service.getOutputs(self.job_id)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 521, in __call__  
return client.invoke(args, kwargs)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 581, in invoke  
result = self.send(soapenv)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 618, in send  
return self.process_reply(reply=content, status=e.httpcode,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\suds\client.py",
line 670, in process_reply  
raise WebFault(fault, replyroot)  
suds.WebFault: Server raised fault: ''  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\ui\gui.py", line 648, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 453, in on_finish  
model_info = self.get_file("ok_models.dat")  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 262, in get_file  
self.get_outputs()  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
chimerax.core.tasks.JobError: Server raised fault: ''  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 300, in get_outputs  
raise JobError(str(e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 5070
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 8,361,205,760
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 4 years ago

Component: Unassigned → Structure Prediction
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Modeller failure

comment:2 by pett, 4 years ago

Resolution: → fixed
Status: accepted → closed

Hi Deepesh,

Thanks for reporting this problem. It turns out that our web server doesn't like the '[' character in the sequence name you are trying to model. Your options are either to edit your alignment file and replace/remove the '[' character, or get tomorrow's 1.3 release candidate or daily build, which will have a fix for this.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by dstnt@…, 4 years ago 

Hi Eric

Thank you for the help! I will probably get tomorrow's 1.3 release candidate to help fix this issue.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, November 2, 2021 1:09 PM
Cc: Sigdel, Deepesh <dstnt@mail.missouri.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #5524: Modeller failure

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#5524: Modeller failure
-------------------------------------------+----------------------------
          Reporter:  dstnt@…               |      Owner:  Eric Pettersen
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  Structure Prediction  |    Version:
        Resolution:  fixed                 |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 Hi Deepesh,
         Thanks for reporting this problem.  It turns out that our web
 server doesn't like the '[' character in the sequence name you are trying
 to model.  Your options are either to edit your alignment file and
 replace/remove the '[' character, or get tomorrow's 1.3 release candidate
 or daily build, which will have a fix for this.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

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