The following bug report has been submitted:
Platform: Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Hi!
When running the built-in Modeller Comparative tool, the log throws the following error after the status bar reporting that the model was built:
<suds.sax.document.Document object at 0x12f5f3150>
Traceback (most recent call last):
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/transport/http.py", line 82, in send
fp = self.u2open(u2request)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/transport/http.py", line 132, in u2open
return url.open(u2request, timeout=tm)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 531, in open
response = meth(req, response)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 641, in http_response
'http', request, response, code, msg, hdrs)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 569, in error
return self._call_chain(*args)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/client.py", line 613, in send
reply = self.options.transport.send(request)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/transport/https.py", line 66, in send
return HttpTransport.send(self, request)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/webservices/opal_job.py", line 297, in get_outputs
r = self._suds.service.getOutputs(self.job_id)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/client.py", line 521, in __call__
return client.invoke(args, kwargs)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/client.py", line 581, in invoke
result = self.send(soapenv)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/client.py", line 619, in send
description=tostr(e), original_soapenv=original_soapenv)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/tasks.py", line 196, in _run_thread
self.run(*args, **kw)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/tasks.py", line 288, in run
self.monitor()
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/modeller/comparative.py", line 393, in monitor
stdout = self.get_file("stdout.txt")
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/webservices/opal_job.py", line 262, in get_file
self.get_outputs()
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 4:
chimerax.core.tasks.JobError: Server raised fault: ''
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 appModeller9v8Service16153794339052050750724 finished
<suds.sax.document.Document object at 0x12f5f37d0>
Traceback (most recent call last):
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/transport/http.py", line 82, in send
fp = self.u2open(u2request)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/transport/http.py", line 132, in u2open
return url.open(u2request, timeout=tm)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 531, in open
response = meth(req, response)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 641, in http_response
'http', request, response, code, msg, hdrs)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 569, in error
return self._call_chain(*args)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/client.py", line 613, in send
reply = self.options.transport.send(request)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/transport/https.py", line 66, in send
return HttpTransport.send(self, request)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/webservices/opal_job.py", line 297, in get_outputs
r = self._suds.service.getOutputs(self.job_id)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/client.py", line 521, in __call__
return client.invoke(args, kwargs)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/client.py", line 581, in invoke
result = self.send(soapenv)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/suds/client.py", line 619, in send
description=tostr(e), original_soapenv=original_soapenv)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/ui/gui.py", line 629, in customEvent
func(*args, **kw)
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/modeller/comparative.py", line 418, in on_finish
model_info = self.get_file("ok_models.dat")
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/webservices/opal_job.py", line 262, in get_file
self.get_outputs()
File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/webservices/opal_job.py", line 300, in get_outputs
raise JobError(str(e))
Thank you for looking into this!
Best
Demian
Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6yvu
6yvu title:
Condensin complex from S.cerevisiae ATP-free apo non-engaged state [more
info...]
Chain information for 6yvu #1
---
Chain | Description
A | Structural maintenance of chromosomes protein 2,Structural maintenance of
chromosomes protein 2,Smc2
B | Structural maintenance of chromosomes protein 4
C | Condensin complex subunit 2,Condensin complex subunit 2,Brn1
D | Condensin complex subunit 1,Condensin complex subunit 1,Ycs4
> ui tool show "Modeller Comparative"
> open
> /Users/demian.keihsler/Projects/cohesin/sequence_alignments_(benedikt)/smc2(yeast)_vs_smc3(human).fasta
Summary of feedback from opening
/Users/demian.keihsler/Projects/cohesin/sequence_alignments_(benedikt)/smc2(yeast)_vs_smc3(human).fasta
---
notes | Alignment identifier is smc2(yeast)_vs_smc3(human).fasta
Associated 6yvu chain A to sp|P38989|SMC2_YEAST Structural maintenance of
chromosomes protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
OX=559292 GN=SMC2 PE=1 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment smc2(yeast)_vs_smc3(human).fasta
Opened 2 sequences from smc2(yeast)_vs_smc3(human).fasta
> modeller comparative smc2(yeast)_vs_smc3(human).fasta:1 multichain true
> numModels 5 fast false hetPreserve false hydrogens false waterPreserve false
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16153785630531741013692
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16153785630531741013692
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service16153785630531741013692 finished
Modeller error output
Traceback (most recent call last):
File "/usr/local/opal-local/bin/modeller9v8.py", line 322, 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 133, in make
self.homcsr(exit_stage)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 595, in homcsr
aln = self.read_alignment()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 556, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 80, in
append
allow_alternates)
_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not
match that in PDB file: 1 ./6yvu_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
MODELLER 9.22, 2019/06/19, r11413
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2019 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 watson.cgl.ucsf.edu
3.10.0-1160.6.1.el7.x86_64 x86_64
Date and time of compilation : 2019/06/19 14:00:54
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/03/10 04:16:03
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL9v22}/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 ${MODINSTALL9v22}/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 ${MODINSTALL9v22}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269801 263.478
0.257
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 284893 278.216
0.272
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300293 293.255
0.286
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331093 323.333
0.316
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392693 383.489
0.375
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 515893 503.802
0.492
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 762293 744.427
0.727
openf___224_> Open ./6yvu_1.pdb
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 771841 753.751
0.736
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 781389 763.075
0.745
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 790937 772.399
0.754
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 800485 781.724
0.763
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 810033 791.048
0.773
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 819581 800.372
0.782
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 829129 809.696
0.791
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 838677 819.021
0.800
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 848225 828.345
0.809
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 857773 837.669
0.818
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 867321 846.993
0.827
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 876869 856.317
0.836
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 886417 865.642
0.845
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 895965 874.966
0.854
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 905513 884.290
0.864
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 915061 893.614
0.873
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 924609 902.938
0.882
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 934157 912.263
0.891
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 943705 921.587
0.900
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 953253 930.911
0.909
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 962801 940.235
0.918
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 972349 949.560
0.927
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 981897 958.884
0.936
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 991445 968.208
0.946
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1000993 977.532
0.955
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1010541 986.856
0.964
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1020089 996.181
0.973
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1029637 1005.505
0.982
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1039185 1014.829
0.991
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1048733 1024.153
1.000
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1058281 1033.478
1.009
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1067829 1042.802
1.018
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1077377 1052.126
1.027
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1086925 1061.450
1.037
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1096473 1070.774
1.046
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1106021 1080.099
1.055
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1115569 1089.423
1.064
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1125117 1098.747
1.073
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1134665 1108.071
1.082
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1144213 1117.396
1.091
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1153761 1126.720
1.100
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1163309 1136.044
1.109
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1172857 1145.368
1.119
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1182405 1154.692
1.128
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1191953 1164.017
1.137
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1201501 1173.341
1.146
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1211049 1182.665
1.155
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1220597 1191.989
1.164
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1230145 1201.313
1.173
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1239693 1210.638
1.182
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1249241 1219.962
1.191
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1258789 1229.286
1.200
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1268337 1238.610
1.210
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1277885 1247.935
1.219
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1287433 1257.259
1.228
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1296981 1266.583
1.237
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1306529 1275.907
1.246
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1316077 1285.231
1.255
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1325625 1294.556
1.264
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./6yvu_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:
MKVEELIIDGFKSYATRTVITDWDPQFNAITGLNGSGKSNILDAICFVLGIASMSTVRASSLQDLIYKRGQAGVT
KASVTIVFDNTDKSNSPIGFTNSPQISVTRQGTSKYLINGHRAPQQSVLQLFQSVQLNINNPNFLIMQGKITKVL
NMKPSEILSLIEEAAGTKMFEDRREKAERTMSKKETKLQENRTLLTEEIEPKLEKLRNEKRMFLEFQSTQTDLEK
TERIVVSYEYYNIKHKHTSIRETLENGETRMKMLNEFVKKTSEEIDSLNEDVEEIKLQKEKELHKSKLENKENGL
LNEISRLKTSLSIKVENLNDTTEKSKALESEIASSSAKLIEKKSAYANTEKDYKMVQEQLSKQRDLYKRKEELVS
TLADGGYNAQLAKAKTELNEVSLAIKKSSMKMELLKKELLTIEPKLKEATKDNELNVKHVKQCQETCDKLRARLV
EYGFDPSRIKDLKQREDKLKSHYYQTCKNSEYLKRRVTNLEFNYTKPYPNFEASFVHGVVGQLFQIDNDNIRYAT
ALQTCAGGRLFNVVVQDSQTATQLLERGRLRKRVTIIPLDKIYTRPISSQVLDLAKKIAPGKVELAINLIRFDES
ITKAMEFIFGNSLICEDPETAKKITFHPKIRARSITLQGDVYDPEGTLSGGSRESLLVDIQKYNQIQKQIETIQA
DLNHVTEELQTQYATSQKTKTIQSDLNLSLHKLDLAKRNLDANPSSQIIARNEEILRDIGECENEIKTKQMSLKK
CQEEVSTIEKDMKEYDSSKLNELKKELKLLAKELEEQESESERKYDLFQNLELETEQLSSELDSNKTLLHNHLKS
IESLKLENSDLEGKIRGVEDDLVTVQTELNEEKKRLMDIDDELNELETLIKKKQDEKKSSELELQKLVHDLNKYK
SNTNNMEKIIEDLDTYRERSKQLNEKFQELRKKVNPNIMNMIENVEKKEAALKTMIKTIEKDKMKIQETISKLNE
YKRETLVKTWEKVTLDFGNIFADLLPNSFAKLVPCEGKDVTQGLEVKVKLGNIWKESLIELSGGQRSLIALSLIM
ALLQFRPAPMYILDEVDAALDLSHTQNIGHLIKTRFKGSQFIVVSLKEGMFANANRVFRTRFQDGTSVV??????
??
PDB sequence matching range provided in alignment:
MKVEELIIDGFKSYATRTVITDWDPQFNAITGLNGSGKSNILDAICFVLGIASMSTVRASSLQDLIYKRGQAGVT
KASVTIVFDNTDKSNSPIGFTNSPQISVTRQGTSKYLINGHRAPQQSVLQLFQSVQLNINNPNFLIMQGKITKVL
NMKPSEILSLIEEAAGTKMFEDRREKAERTMSKKETKLQENRTLLTEEIEPKLEKLRNEKRMFLEFQSTQTDLEK
TERIVVSYEYYNIKHKHTSIRETLENGETRMKMLNEFVKKTSEEIDSLNEDVEEIKLQKEKELHKSKLENKENGL
LNEISRLKTSLSIKVENLNDTTEKSKALESEIASSSAKLIEKKSAYANTEKDYKMVQEQLSKQRDLYKRKEELVS
TLADGGYNAQLAKAKTELNEVSLAIKKSSMKMELLKKELLTIEPKLKEATKDNELNVKHVKQCQETCDKLRARLV
EYGFDPSRIKDLKQREDKLKSHYYQTCKNSEYLKRRVTNLEFNYTKPYPNFEASFVHGVVGQLFQIDNDNIRYAT
ALQTCAGGRLFNVVVQDSQTATQLLERGRLRKRVTIIPLDKIYTRPISSQVLDLAKKIAPGKVELAINLIRFDES
ITKAMEFIFGNSLICEDPETAKKITFHPKIRARSITLQGDVYDPEGTLSGGSRESLLVDIQKYNQIQKQIETIQA
DLNHVTEELQTQYATSQKTKTIQSDLNLSLHKLDLAKRNLDANPSSQIIARNEEILRDIGECENEIKTKQMSLKK
CQEEVSTIEKDMKEYDSSKLNELKKELKLLAKELEEQESESERKYDLFQNLELETEQLSSELDSNKTLLHNHLKS
IESLKLENSDLEGKIRGVEDDLVTVQTELNEEKKRLMDIDDELNELETLIKKKQDEKKSSELELQKLVHDLNKYK
SNTNNMEKIIEDLDTYRERSKQLNEKFQELRKKVNPNIMNMIENVEKKEAALKTMIKTIEKDKMKIQETISKLNE
YKRETLVKTWEKVTLDFGNIFADLLPNSFAKLVPCEGKDVTQGLEVKVKLGNIWKESLIELSGGQRSLIALSLIM
ALLQFRPAPMYILDEVDAALDLSHTQNIGHLIKTRFKGSQFIVVSLKEGMFANANRVFRTRFQDGTSVVXXXXXX
XXQSRLFINELVLENFKSYAGKQVVGPFHTSFSAVVGPNGSGKSNVIDSMLFVFGFRANKMRQDRLSDLIHKSEA
FPSLQSCSVAVHFQYVIDESSGTSRIDEEKPGLIITRKAFKNNSSKYYINEKESSYTEVTKLLKNEGIDLDHKRF
LILQGEVENIAQMKPKAEKESDDGLLEYLEDIIGTANYKPLIEERMGQIENLNEVCLEKENRFEIVDREKNSLES
GKETALEFLEKEKQLTLLRSKLFQFKLLQSNSKLASTLEKISSSNKDLEDEKMKFQESLKKVDEIKAQRKEIKDR
ISSCSSKEKTLVLERRELEGTRVSLEERTKNLVSKMEKAEKTLKSTKHSISEAENMLEELRGQQTEHETEIKDLT
QLLEKERSILDDIKLSLKDKTKNISAEIIRHEKELEPWDLQLQEKESQIQLAESELSLLEETQAKLKKNVETLEE
KILAKKTHKQELQDLILDLKKKLNSLKDERSQGEKNFTSAHLKLKEMQKVLNAHRQRAMEARSSLSKAQNKSKVL
TALSRLQKSGRINGFHGRLGDLGVIDDSFDVAISTACPRLDDVVVDTVECAQHCIDYLRKNKLGYARFILLDRLR
QFNLQPISTPENVPRLFDLVKPKNPKFSNAFYSVLRDTLVAQNLKQANNVAYGKKRFRVVTVDGKLIDISGTMSG
GGNHVAKGLMKLKVDDYTPEEVDKIERELSERENNFRVASDTVHEMEEELKKLRDHEPDLESQISKAEMEADSLA
SELTLAEQQVKEAEMAYVKAVSDKAQLNVVMKNLERLRGEYNDLQSETKTKKEKIKGLQDEIMKIIKLQMQNSKV
ESVCQKLDILVAKLKKVKSASKKSGGDVVKFQKLLQNSERDVELSSDELKVIEEQLKHTKLALAENDTNMNETLN
LKVELKEQSEQLKEQMEDMEESINEFKSIEIEMKNKLEKLNSLLTYIKSEITQQEKGLESEIKDAETSCLSEDEL
RELDVELIESKINELSYYVEETNVDIGVLEEYARRLAEFKRRKLDLNNAVQKRDEVKEQLGILKKKRFDEFMAGF
NIISMTLKEMYQMITMGGNAELELVDSLDPFSEGVTFSVMPPKKSWRNITNLSGGEKTLSSLALVFALHKYKPTP
LYVMDEIDAALDFRNVSIVANYIKERTKNAQFIVISLRNNMFELAQQLVGVYKRDNRTKSTTIKNIDISTMMANF
EEWIKMATDNKINSRNSWNFALIDYFYDLDVLKDGENNINFQKASATLDGCIKIYSSRVDSVTTETGKLLSGLAQ
RKTLVEFETIKIDPLFKKALVDFGAKSLLLNTLNIDNTARVIFDAKKVDVRRLKKNVWRSINNLIQEHDSRESTK
ELKFSDIIQGISKMYSDDTLKDISTSFCFICLLHLANEHGLQITHTENYNDLIVNYEDLXXXXXXXXXXXXXXXX
XXXSLSEYLTKFRELNVIIDQSPDSLEALIDLCHSSLSNLSKDIKANLSSNVNFTEGLIPQWKRHLEEYGYLIQV
LLTFLQMENLLESITKLLEINPEKDLFIGLFTRPLFVLLKMFIQRILAMCVKNHGQSSSIQSSLMTNLTYFLHLS
VFNAELLKLLNDEYNYPQLTEDILKEISTRVFNAKDTTGPKAISNFLIKLSELSPGIMLRQMNLVITLLNNSSIT
LRCSVVEACGNIVAELAQDPQTMEHYKQQIAVLIELLEERFQDSNPYVRTKAIQGCSKICDLSSKFNKSKAKFTS
LAVRSLQDRSSLVRRNSVKLLSKLLLKHPFKAIHGSQLRLSEWEEYLKGSESQLNSTSVLMKLKLMIVYYKDAIS
FIKEIHKSIELISNLLFNRNEVLESMDFLVLADAFDIELSEFGIKKMLHLVWISVHLIECYKQLFLTAPDSCNMQ
EKAAHIAKNLINLSIGASIADLASLEQLLGMMYEQKLIDQHVINILWAIYNSASKGFSKEQIHGSIIILGMLSLA
DNEIALKGLESLLNIGLGAVGLKDLTLCRYSCLALERMVPQELEDVAVKKLYAIIINYTKDNEYYPMCEQALSAL
FTISSKPDILATDLIREKTMMVVSLSQLLFIVGQVAIKTLVYLEKCEAEFKKRKIDKELEMIGGTNEDFTDAIQF
VKENMLQRTATLCLEKLMCLSSKYCEKSLPLLITVMEKSPDPTIRSNAVLGLGDMAVCVDENTDYLYRRLHDENL
MVQRTCLMTVTFLILAGQGQLGEMAKCLDNPDQGISDMCRLFFTELASGFIDIFSNLSSDDLLGKESFKKIIKFL
LTFIDKERHQKQLNEKLVGRLRKCETQKQWDDIAFXXXXXXXXX
No output models from Modeller; see log for Modeller text output.
> select /A
7522 atoms, 7589 bonds, 7 pseudobonds, 1127 residues, 2 models selected
> select /D
6744 atoms, 6821 bonds, 20 pseudobonds, 866 residues, 2 models selected
> select /A
7522 atoms, 7589 bonds, 7 pseudobonds, 1127 residues, 2 models selected
> select ~sel
16694 atoms, 16869 bonds, 30 pseudobonds, 2292 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> ui tool show "Modeller Comparative"
> modeller comparative smc2(yeast)_vs_smc3(human).fasta:1 multichain true
> numModels 5 fast false hetPreserve false hydrogens false waterPreserve false
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16153787378211259614213
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16153787378211259614213
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service16153787378211259614213 finished
Modeller error output
Traceback (most recent call last):
File "/usr/local/opal-local/bin/modeller9v8.py", line 322, 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 133, in make
self.homcsr(exit_stage)
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 595, in homcsr
aln = self.read_alignment()
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 556, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 80, in
append
allow_alternates)
_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not
match that in PDB file: 1 ./6yvu_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
MODELLER 9.22, 2019/06/19, r11413
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2019 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 watson.cgl.ucsf.edu
3.10.0-1160.6.1.el7.x86_64 x86_64
Date and time of compilation : 2019/06/19 14:00:54
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2021/03/10 04:18:57
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL9v22}/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 ${MODINSTALL9v22}/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 ${MODINSTALL9v22}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269801 263.478
0.257
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 284893 278.216
0.272
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300293 293.255
0.286
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331093 323.333
0.316
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392693 383.489
0.375
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 515893 503.802
0.492
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 762293 744.427
0.727
openf___224_> Open ./6yvu_1.pdb
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./6yvu_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:
MKVEELIIDGFKSYATRTVITDWDPQFNAITGLNGSGKSNILDAICFVLGIASMSTVRASSLQDLIYKRGQAGVT
KASVTIVFDNTDKSNSPIGFTNSPQISVTRQGTSKYLINGHRAPQQSVLQLFQSVQLNINNPNFLIMQGKITKVL
NMKPSEILSLIEEAAGTKMFEDRREKAERTMSKKETKLQENRTLLTEEIEPKLEKLRNEKRMFLEFQSTQTDLEK
TERIVVSYEYYNIKHKHTSIRETLENGETRMKMLNEFVKKTSEEIDSLNEDVEEIKLQKEKELHKSKLENKENGL
LNEISRLKTSLSIKVENLNDTTEKSKALESEIASSSAKLIEKKSAYANTEKDYKMVQEQLSKQRDLYKRKEELVS
TLADGGYNAQLAKAKTELNEVSLAIKKSSMKMELLKKELLTIEPKLKEATKDNELNVKHVKQCQETCDKLRARLV
EYGFDPSRIKDLKQREDKLKSHYYQTCKNSEYLKRRVTNLEFNYTKPYPNFEASFVHGVVGQLFQIDNDNIRYAT
ALQTCAGGRLFNVVVQDSQTATQLLERGRLRKRVTIIPLDKIYTRPISSQVLDLAKKIAPGKVELAINLIRFDES
ITKAMEFIFGNSLICEDPETAKKITFHPKIRARSITLQGDVYDPEGTLSGGSRESLLVDIQKYNQIQKQIETIQA
DLNHVTEELQTQYATSQKTKTIQSDLNLSLHKLDLAKRNLDANPSSQIIARNEEILRDIGECENEIKTKQMSLKK
CQEEVSTIEKDMKEYDSSKLNELKKELKLLAKELEEQESESERKYDLFQNLELETEQLSSELDSNKTLLHNHLKS
IESLKLENSDLEGKIRGVEDDLVTVQTELNEEKKRLMDIDDELNELETLIKKKQDEKKSSELELQKLVHDLNKYK
SNTNNMEKIIEDLDTYRERSKQLNEKFQELRKKVNPNIMNMIENVEKKEAALKTMIKTIEKDKMKIQETISKLNE
YKRETLVKTWEKVTLDFGNIFADLLPNSFAKLVPCEGKDVTQGLEVKVKLGNIWKESLIELSGGQRSLIALSLIM
ALLQFRPAPMYILDEVDAALDLSHTQNIGHLIKTRFKGSQFIVVSLKEGMFANANRVFRTRFQDGTSVV??????
??
PDB sequence matching range provided in alignment:
MKVEELIIDGFKSYATRTVITDWDPQFNAITGLNGSGKSNILDAICFVLGIASMSTVRASSLQDLIYKRGQAGVT
KASVTIVFDNTDKSNSPIGFTNSPQISVTRQGTSKYLINGHRAPQQSVLQLFQSVQLNINNPNFLIMQGKITKVL
NMKPSEILSLIEEAAGTKMFEDRREKAERTMSKKETKLQENRTLLTEEIEPKLEKLRNEKRMFLEFQSTQTDLEK
TERIVVSYEYYNIKHKHTSIRETLENGETRMKMLNEFVKKTSEEIDSLNEDVEEIKLQKEKELHKSKLENKENGL
LNEISRLKTSLSIKVENLNDTTEKSKALESEIASSSAKLIEKKSAYANTEKDYKMVQEQLSKQRDLYKRKEELVS
TLADGGYNAQLAKAKTELNEVSLAIKKSSMKMELLKKELLTIEPKLKEATKDNELNVKHVKQCQETCDKLRARLV
EYGFDPSRIKDLKQREDKLKSHYYQTCKNSEYLKRRVTNLEFNYTKPYPNFEASFVHGVVGQLFQIDNDNIRYAT
ALQTCAGGRLFNVVVQDSQTATQLLERGRLRKRVTIIPLDKIYTRPISSQVLDLAKKIAPGKVELAINLIRFDES
ITKAMEFIFGNSLICEDPETAKKITFHPKIRARSITLQGDVYDPEGTLSGGSRESLLVDIQKYNQIQKQIETIQA
DLNHVTEELQTQYATSQKTKTIQSDLNLSLHKLDLAKRNLDANPSSQIIARNEEILRDIGECENEIKTKQMSLKK
CQEEVSTIEKDMKEYDSSKLNELKKELKLLAKELEEQESESERKYDLFQNLELETEQLSSELDSNKTLLHNHLKS
IESLKLENSDLEGKIRGVEDDLVTVQTELNEEKKRLMDIDDELNELETLIKKKQDEKKSSELELQKLVHDLNKYK
SNTNNMEKIIEDLDTYRERSKQLNEKFQELRKKVNPNIMNMIENVEKKEAALKTMIKTIEKDKMKIQETISKLNE
YKRETLVKTWEKVTLDFGNIFADLLPNSFAKLVPCEGKDVTQGLEVKVKLGNIWKESLIELSGGQRSLIALSLIM
ALLQFRPAPMYILDEVDAALDLSHTQNIGHLIKTRFKGSQFIVVSLKEGMFANANRVFRTRFQDGTSVVXXXXXX
XX
No output models from Modeller; see log for Modeller text output.
> select ::name="UNK"
40 atoms, 39 bonds, 8 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Modeller Comparative"
> modeller comparative smc2(yeast)_vs_smc3(human).fasta:1 multichain true
> numModels 5 fast false hetPreserve false hydrogens false waterPreserve false
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16153788860952023674325
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16153788860952023674325
stdout.txt = standard output
stderr.txt = standard error
<suds.sax.document.Document object at 0x12fefe390>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 82, in send
fp = self.u2open(u2request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 132, in u2open
return url.open(u2request, timeout=tm)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 531, in open
response = meth(req, response)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 641, in http_response
'http', request, response, code, msg, hdrs)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 569, in error
return self._call_chain(*args)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain
result = func(*args)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 613, in send
reply = self.options.transport.send(request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/https.py", line 66, in send
return HttpTransport.send(self, request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 297, in get_outputs
r = self._suds.service.getOutputs(self.job_id)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 521, in __call__
return client.invoke(args, kwargs)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 581, in invoke
result = self.send(soapenv)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 619, in send
description=tostr(e), original_soapenv=original_soapenv)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread
self.run(*args, **kw)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 288, in run
self.monitor()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/modeller/comparative.py", line 393, in monitor
stdout = self.get_file("stdout.txt")
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 262, in get_file
self.get_outputs()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 3:
chimerax.core.tasks.JobError: Server raised fault: ''
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 appModeller9v8Service16153788860952023674325 finished
<suds.sax.document.Document object at 0x131564390>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 82, in send
fp = self.u2open(u2request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 132, in u2open
return url.open(u2request, timeout=tm)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 531, in open
response = meth(req, response)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 641, in http_response
'http', request, response, code, msg, hdrs)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 569, in error
return self._call_chain(*args)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain
result = func(*args)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 613, in send
reply = self.options.transport.send(request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/https.py", line 66, in send
return HttpTransport.send(self, request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 297, in get_outputs
r = self._suds.service.getOutputs(self.job_id)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 521, in __call__
return client.invoke(args, kwargs)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 581, in invoke
result = self.send(soapenv)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 619, in send
description=tostr(e), original_soapenv=original_soapenv)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 629, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/modeller/comparative.py", line 418, in on_finish
model_info = self.get_file("ok_models.dat")
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 262, in get_file
self.get_outputs()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 300, in get_outputs
raise JobError(str(e))
See log for complete Python traceback.
> ui tool show "Modeller Comparative"
> modeller comparative smc2(yeast)_vs_smc3(human).fasta:1 multichain true
> numModels 5 fast true hetPreserve false hydrogens false waterPreserve false
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16153794339052050750724
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16153794339052050750724
stdout.txt = standard output
stderr.txt = standard error
<suds.sax.document.Document object at 0x12f5f3150>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 82, in send
fp = self.u2open(u2request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 132, in u2open
return url.open(u2request, timeout=tm)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 531, in open
response = meth(req, response)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 641, in http_response
'http', request, response, code, msg, hdrs)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 569, in error
return self._call_chain(*args)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain
result = func(*args)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 613, in send
reply = self.options.transport.send(request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/https.py", line 66, in send
return HttpTransport.send(self, request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 297, in get_outputs
r = self._suds.service.getOutputs(self.job_id)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 521, in __call__
return client.invoke(args, kwargs)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 581, in invoke
result = self.send(soapenv)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 619, in send
description=tostr(e), original_soapenv=original_soapenv)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread
self.run(*args, **kw)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 288, in run
self.monitor()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/modeller/comparative.py", line 393, in monitor
stdout = self.get_file("stdout.txt")
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 262, in get_file
self.get_outputs()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 4:
chimerax.core.tasks.JobError: Server raised fault: ''
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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 appModeller9v8Service16153794339052050750724 finished
<suds.sax.document.Document object at 0x12f5f37d0>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 82, in send
fp = self.u2open(u2request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 132, in u2open
return url.open(u2request, timeout=tm)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 531, in open
response = meth(req, response)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 641, in http_response
'http', request, response, code, msg, hdrs)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 569, in error
return self._call_chain(*args)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain
result = func(*args)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 613, in send
reply = self.options.transport.send(request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/https.py", line 66, in send
return HttpTransport.send(self, request)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 297, in get_outputs
r = self._suds.service.getOutputs(self.job_id)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 521, in __call__
return client.invoke(args, kwargs)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 581, in invoke
result = self.send(soapenv)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 619, in send
description=tostr(e), original_soapenv=original_soapenv)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 629, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/modeller/comparative.py", line 418, in on_finish
model_info = self.get_file("ok_models.dat")
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 262, in get_file
self.get_outputs()
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 300, in get_outputs
raise JobError(str(e))
See log for complete Python traceback.
> ui tool show "Modeller Comparative"
> help help:contact.html
OpenGL version: 4.1 INTEL-12.10.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 1554.80.3.0.0 (iBridge: 18.16.14346.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G6042)
Kernel Version: Darwin 18.7.0
Time since boot: 2:50
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
LG TV:
Resolution: 3360 x 2100
UI Looks like: 1680 x 1050 @ 24 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.26
Television: Yes
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
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: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
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: 0.29.20
decorator: 4.4.2
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: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Demian,
--Eric