Opened 5 years ago

Last modified 5 years ago

#4264 accepted defect

Modeller: cannot handle direction association onto target if deletions in target

Reported by: david.haselbach@… Owned by: Eric Pettersen
Priority: moderate Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 I want to make comparative modelling of AAA protein. Unfortunately I am running into errors. Here are the commands I used:
open P32794 fromDatabase uniprot
open 6opc
sequence associate /A P32794
sequence associate /B P32794
sequence associate /C P32794
sequence associate /D P32794
sequence associate /E P32794
sequence associate /F P32794
modeller comparative P32794:1 multichain true numModels 5 fast false hetPreserve true hydrogens false waterPreserve false

This is the result: 
get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./6opc_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).

I see that there are regions where the alignment didnt work. So I wanted to select a subsequence However I couldnt quite figure out the right syntax. 

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 P32794 fromDatabase uniprot

Summary of feedback from opening P32794 fetched from uniprot  
---  
note | Alignment identifier is P32794  
  
Opened UniProt P32794  

> open 6opc

Summary of feedback from opening 6opc fetched from pdb  
---  
warnings | Atom CG1 is not in the residue template for UNK /G:14  
Atom CG1 is not in the residue template for UNK /G:16  
Atom CG1 is not in the residue template for UNK /G:18  
Atom CG1 is not in the residue template for UNK /G:20  
  
6opc title:  
Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) [more info...]  
  
Chain information for 6opc #1  
---  
Chain | Description  
A B C D E F | Cell division control protein 48  
G | Substrate bound to the central pore of the Cdc48 hexamer  
Z | UBX domain-containing protein 1  
  
Non-standard residues in 6opc #1  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
  
Associated 6opc chain G to P32794 with 0 mismatches  

> sequence associate #6/F P32794

> sequence associate /A P32794

Associated 6opc chain A to P32794 with 543 mismatches and/or gaps  

> sequence associate /B P32794

Associated 6opc chain B to P32794 with 543 mismatches and/or gaps  

> sequence associate /C P32794

Associated 6opc chain C to P32794 with 543 mismatches and/or gaps  

> sequence associate /D P32794

Associated 6opc chain D to P32794 with 543 mismatches and/or gaps  

> sequence associate /E P32794

Associated 6opc chain E to P32794 with 543 mismatches and/or gaps  

> sequence associate /F P32794

Associated 6opc chain F to P32794 with 543 mismatches and/or gaps  

> ui tool show "Modeller Comparative"

> modeller comparative P32794:1 multichain true numModels 5 fast false
> hetPreserve true 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: appModeller9v8Service1613596329188-291859351  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1613596329188-291859351  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1613596329188-291859351 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 69, 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 ./6opc_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): 2021/02/17 13:12:09  
  
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  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1255093 1225.677
1.197  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 2240693 2188.177
2.137  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4211893 4113.177
4.017  
openf___224_> Open ./6opc_1.pdb  
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./6opc_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:  
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIR  
LGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP  
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYG  
PPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV  
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVD  
LEALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKF  
GLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDS  
IAKARGAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQL  
RKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKT  
AKRSVSDAELRRYEAYSQQMKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDD  
ELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGD  
HFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLR  
HPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAI  
IFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDAT  
GRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIK  
EELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRD  
IFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRL  
DQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDP  
VPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDK  
LELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTI  
EGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNM  
NEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPE  
VMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATN  
RPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQI  
RPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATE  
VSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMN  
AKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADL  
LYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFK  
KDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRL  
GDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPE  
EYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGP  
PGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVE  
RRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDL  
EALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFG  
LSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSI  
AKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQ  
LRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTAKRSVS  
DAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVL  
IVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYR  
PVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREM  
VELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAE  
KNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDI  
GIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRSVNVTWDDVGGLDEIKEELK  
ETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDK  
ARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLI  
YVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAEAMKTAK  
RSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRK  
DTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFV  
EAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGCRKQMAQIREMVELPLRHPQLFKAIGIKP  
PRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDK  
TNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGDATGRLEVLRIHTKNMKLAD  
DVDLEALAAETHGYVGADIASLCSEAAMQQIRTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFKGVLFYGPTGK  
TLLAKAVATEVSANFISVKGPELLGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLT  
EMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSG  
ADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM???  
???????????????????  
  
PDB sequence matching range provided in alignment:  
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIR  
LGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP  
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYG  
PPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV  
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVD  
LEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE  
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGP  
ELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGAT  
NRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYA  
IKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKKDNMLLVDDAINDDNS  
VIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYAT  
RISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGE  
PINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANET  
GAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKA  
RSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIA  
SLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKE  
ELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDI  
FDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPG  
RLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAE  
DPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTM  
DKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIAD  
TIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEEN  
NMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLING  
PEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAA  
TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQ  
QIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYP  
VLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAP  
TVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVP  
LPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKE  
HFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGD  
TVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNL  
FDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDD  
IGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAG  
ESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDP  
ALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLI  
DLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTK  
FGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELD  
SIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLS  
ILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTA  
KRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKR  
KDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYF  
VEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMA  
QIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKA  
FEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFD  
REVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDA  
EVLDSLGVTMDNFRFALGNSVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTL  
LAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVV  
NQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIA  
KATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKD  
NMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGD  
LVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEY  
AVVAQDTIIHWEGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLIN  
GPEVMSGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATN  
RPNSIDPALRRFGRFDREVDIGDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRE  
KMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFKGVLFYGP  
TGKTLLAKAVATEVSANFISVKGPELLGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRV  
VNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVDENARLSILNAQLRKTPLEPGLELTAIAKA  
TQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYS  
QQMXXXXXXXXXXXXXXXXXXXXXXSSPAEVPKNETPAAQEQPMPDNEPKQGDTSIQIRYANGKREVLHCNSTDT  
VKFLYEHVTSNANTDPSRNFTLNYAFPIKPISNDETTLKDADLLNSVVVQRW&.$&.$&$&.$.&.$&.$&.$&.  
$&&  
  
No output models from Modeller; see log for Modeller text output.  

> ui tool show "Modeller Comparative"

> modeller comparative P32794:1 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: appModeller9v8Service1613596477964451329980  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1613596477964451329980  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1613596477964451329980 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 ./6opc_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): 2021/02/17 13:14:38  
  
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  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1255093 1225.677
1.197  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 2240693 2188.177
2.137  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4211893 4113.177
4.017  
openf___224_> Open ./6opc_1.pdb  
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./6opc_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:  
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIR  
LGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP  
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYG  
PPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV  
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVD  
LEALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKF  
GLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDS  
IAKARGAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQL  
RKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKT  
AKRSVSDAELRRYEAYSQQMKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDD  
ELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGD  
HFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLR  
HPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAI  
IFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDAT  
GRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIK  
EELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRD  
IFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRL  
DQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDP  
VPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDK  
LELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTI  
EGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNM  
NEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPE  
VMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATN  
RPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQI  
RPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATE  
VSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMN  
AKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADL  
LYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFK  
KDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRL  
GDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPE  
EYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGP  
PGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVE  
RRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDL  
EALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFG  
LSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSI  
AKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQ  
LRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTAKRSVS  
DAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVL  
IVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYR  
PVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREM  
VELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAE  
KNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDI  
GIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRSVNVTWDDVGGLDEIKEELK  
ETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDK  
ARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLI  
YVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAEAMKTAK  
RSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRK  
DTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFV  
EAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGCRKQMAQIREMVELPLRHPQLFKAIGIKP  
PRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDK  
TNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGDATGRLEVLRIHTKNMKLAD  
DVDLEALAAETHGYVGADIASLCSEAAMQQIRTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFKGVLFYGPTGK  
TLLAKAVATEVSANFISVKGPELLGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLT  
EMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSG  
ADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM???  
???????????????????  
  
PDB sequence matching range provided in alignment:  
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIR  
LGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP  
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYG  
PPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV  
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVD  
LEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE  
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGP  
ELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGAT  
NRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYA  
IKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKKDNMLLVDDAINDDNS  
VIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYAT  
RISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGE  
PINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANET  
GAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKA  
RSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIA  
SLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKE  
ELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDI  
FDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPG  
RLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAE  
DPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTM  
DKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIAD  
TIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEEN  
NMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLING  
PEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAA  
TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQ  
QIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYP  
VLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAP  
TVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVP  
LPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKE  
HFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGD  
TVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNL  
FDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDD  
IGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAG  
ESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDP  
ALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLI  
DLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTK  
FGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELD  
SIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLS  
ILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTA  
KRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKR  
KDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYF  
VEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMA  
QIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKA  
FEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFD  
REVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDA  
EVLDSLGVTMDNFRFALGNSVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTL  
LAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVV  
NQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIA  
KATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKD  
NMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGD  
LVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEY  
AVVAQDTIIHWEGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLIN  
GPEVMSGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATN  
RPNSIDPALRRFGRFDREVDIGDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRE  
KMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFKGVLFYGP  
TGKTLLAKAVATEVSANFISVKGPELLGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRV  
VNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVDENARLSILNAQLRKTPLEPGLELTAIAKA  
TQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYS  
QQMXXXXXXXXXXXXXXXXXXXXXXSSPAEVPKNETPAAQEQPMPDNEPKQGDTSIQIRYANGKREVLHCNSTDT  
VKFLYEHVTSNANTDPSRNFTLNYAFPIKPISNDETTLKDADLLNSVVVQRW  
  
No output models from Modeller; see log for Modeller text output.  

> modeller comparative P32794:230-709 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Missing or invalid "targets" argument: No sequence named '230-709' found in
alignment  

> modeller comparative P32794/A:230-709 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Missing or invalid "targets" argument: No known alignment with ID: 'P32794/A'  

> modeller comparative P32794 230-709 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Expected a keyword  

> modeller comparative "P32794 230-709" multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false

Missing or invalid "targets" argument: No sequences match 'P32794 230-709'  

> ui tool show "Modeller Comparative"

> modeller comparative P32794:1 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: appModeller9v8Service16135979643211949792296  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16135979643211949792296  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service16135979643211949792296 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 ./6opc_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): 2021/02/17 13:39:24  
  
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  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1255093 1225.677
1.197  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 2240693 2188.177
2.137  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4211893 4113.177
4.017  
openf___224_> Open ./6opc_1.pdb  
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./6opc_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:  
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIR  
LGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP  
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYG  
PPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV  
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVD  
LEALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKF  
GLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDS  
IAKARGAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQL  
RKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKT  
AKRSVSDAELRRYEAYSQQMKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDD  
ELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGD  
HFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLR  
HPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAI  
IFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDAT  
GRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIK  
EELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRD  
IFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRL  
DQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDP  
VPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDK  
LELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTI  
EGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNM  
NEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPE  
VMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATN  
RPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQI  
RPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATE  
VSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMN  
AKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADL  
LYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFK  
KDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRL  
GDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPE  
EYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGP  
PGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVE  
RRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDL  
EALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFG  
LSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSI  
AKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQ  
LRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTAKRSVS  
DAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVL  
IVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYR  
PVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREM  
VELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAE  
KNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDI  
GIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRSVNVTWDDVGGLDEIKEELK  
ETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDK  
ARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLI  
YVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAEAMKTAK  
RSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRK  
DTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFV  
EAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGCRKQMAQIREMVELPLRHPQLFKAIGIKP  
PRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDK  
TNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGDATGRLEVLRIHTKNMKLAD  
DVDLEALAAETHGYVGADIASLCSEAAMQQIRTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFKGVLFYGPTGK  
TLLAKAVATEVSANFISVKGPELLGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSAGGASDRVVNQLLT  
EMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSG  
ADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM???  
???????????????????  
  
PDB sequence matching range provided in alignment:  
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIR  
LGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP  
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYG  
PPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV  
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVD  
LEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE  
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGP  
ELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGAT  
NRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYA  
IKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKKDNMLLVDDAINDDNS  
VIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYAT  
RISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGE  
PINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANET  
GAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKA  
RSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIA  
SLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKE  
ELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDI  
FDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPG  
RLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAE  
DPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTM  
DKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIAD  
TIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEEN  
NMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLING  
PEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAA  
TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQ  
QIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYP  
VLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAP  
TVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVP  
LPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKE  
HFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGD  
TVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNL  
FDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDD  
IGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAG  
ESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDP  
ALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLI  
DLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTK  
FGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELD  
SIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLS  
ILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTA  
KRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKR  
KDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYF  
VEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMA  
QIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKA  
FEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFD  
REVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDA  
EVLDSLGVTMDNFRFALGNSVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTL  
LAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVV  
NQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIA  
KATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKD  
NMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGD  
LVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEY  
AVVAQDTIIHWEGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLIN  
GPEVMSGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATN  
RPNSIDPALRRFGRFDREVDIGDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRE  
KMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFKGVLFYGP  
TGKTLLAKAVATEVSANFISVKGPELLGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRV  
VNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVDENARLSILNAQLRKTPLEPGLELTAIAKA  
TQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYS  
QQMXXXXXXXXXXXXXXXXXXXXXXSSPAEVPKNETPAAQEQPMPDNEPKQGDTSIQIRYANGKREVLHCNSTDT  
VKFLYEHVTSNANTDPSRNFTLNYAFPIKPISNDETTLKDADLLNSVVVQRW  
  
No output models from Modeller; see log for Modeller text output.  

> ui tool show "Show Sequence Viewer"

> delete atoms sel

> delete bonds sel

> delete atoms

> delete bonds

> open 6opc format mmcif fromDatabase pdb

Summary of feedback from opening 6opc fetched from pdb  
---  
warnings | Atom CG1 is not in the residue template for UNK /G:14  
Atom CG1 is not in the residue template for UNK /G:16  
Atom CG1 is not in the residue template for UNK /G:18  
Atom CG1 is not in the residue template for UNK /G:20  
  
6opc title:  
Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) [more info...]  
  
Chain information for 6opc #1  
---  
Chain | Description  
A B C D E F | Cell division control protein 48  
G | Substrate bound to the central pore of the Cdc48 hexamer  
Z | UBX domain-containing protein 1  
  
Non-standard residues in 6opc #1  
---  
ADP — adenosine-5'-diphosphate  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
  
Associated 6opc chain G to P32794 with 0 mismatches  

> sequence associate /A P32794:1

Associated 6opc chain A to P32794 with 543 mismatches and/or gaps  

> ui tool show "Modeller Comparative"

> modeller comparative P32794:1 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: appModeller9v8Service1613598292560-2056085634  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1613598292560-2056085634  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1613598292560-2056085634 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 ./6opc_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): 2021/02/17 13:44:52  
  
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  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1255093 1225.677
1.197  
openf___224_> Open ./6opc_1.pdb  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1264641 1235.001
1.206  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1274189 1244.325
1.215  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1283737 1253.649
1.224  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1293285 1262.974
1.233  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1302833 1272.298
1.242  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1312381 1281.622
1.252  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1321929 1290.946
1.261  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1331477 1300.271
1.270  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1341025 1309.595
1.279  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1350573 1318.919
1.288  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1360121 1328.243
1.297  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1369669 1337.567
1.306  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1379217 1346.892
1.315  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1388765 1356.216
1.324  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1398313 1365.540
1.334  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1407861 1374.864
1.343  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1417409 1384.188
1.352  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1426957 1393.513
1.361  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1436505 1402.837
1.370  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1446053 1412.161
1.379  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1455601 1421.485
1.388  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1465149 1430.810
1.397  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1474697 1440.134
1.406  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1484245 1449.458
1.415  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1493793 1458.782
1.425  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1503341 1468.106
1.434  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1512889 1477.431
1.443  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1522437 1486.755
1.452  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1531985 1496.079
1.461  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1541533 1505.403
1.470  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1551081 1514.728
1.479  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1560629 1524.052
1.488  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1570177 1533.376
1.497  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1579725 1542.700
1.507  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1589273 1552.024
1.516  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1598821 1561.349
1.525  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1608369 1570.673
1.534  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1617917 1579.997
1.543  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1627465 1589.321
1.552  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1637013 1598.646
1.561  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1646561 1607.970
1.570  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1656109 1617.294
1.579  
get_ran_648E> Alignment sequence does not match that in PDB file: 1
./6opc_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:  
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIR  
LGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP  
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYG  
PPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV  
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVD  
LEALAAETHGYVGADIASLCSEAAMQQIRPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKF  
GLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDS  
IAKARGAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQL  
RKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKT  
AKRSVSDAELRRYEAYSQQM??????????????????????  
  
PDB sequence matching range provided in alignment:  
KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIR  
LGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP  
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYG  
PPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV  
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVD  
LEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE  
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGP  
ELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGAT  
NRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYA  
IKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKKDNMLLVDDAINDDNS  
VIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYAT  
RISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGE  
PINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANET  
GAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKA  
RSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIA  
SLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKE  
ELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDI  
FDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPG  
RLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAE  
DPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTM  
DKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIAD  
TIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEEN  
NMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLING  
PEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAA  
TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQ  
QIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYP  
VLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAP  
TVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVP  
LPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKE  
HFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGD  
TVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNL  
FDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDD  
IGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAG  
ESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDP  
ALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLI  
DLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTK  
FGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELD  
SIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLS  
ILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEDPVPYITKEHFAEAMKTA  
KRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKR  
KDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYF  
VEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMA  
QIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKA  
FEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFD  
REVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDA  
EVLDSLGVTMDNFRFALGNSVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTL  
LAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVV  
NQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIA  
KATQGFSGADLLYIVQRAAKYAIKDSIYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFKKD  
NMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGD  
LVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEY  
AVVAQDTIIHWEGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLIN  
GPEVMSGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATN  
RPNSIDPALRRFGRFDREVDIGDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIRE  
KMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFKGVLFYGP  
TGKTLLAKAVATEVSANFISVKGPELLGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRV  
VNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVDENARLSILNAQLRKTPLEPGLELTAIAKA  
TQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYS  
QQMXXXXXXXXXXXXXXXXXXXXXXSSPAEVPKNETPAAQEQPMPDNEPKQGDTSIQIRYANGKREVLHCNSTDT  
VKFLYEHVTSNANTDPSRNFTLNYAFPIKPISNDETTLKDADLLNSVVVQRW  
  
No output models from Modeller; see log for Modeller text output.  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Intel Core i7
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 198.71.1.0.0
      SMC Version (system): 2.45f0

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G87)
      Kernel Version: Darwin 18.7.0
      Time since boot: 16 days 13:30

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560:

      Chipset Model: Radeon Pro 560
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c0
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AU-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    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

Attachments (1)

realigned.afasta​ (1.8 KB ) - added by Eric Pettersen 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Modeller: sequence mismatch to structure

in reply to:  2 ; comment:2 by Eric Pettersen, 5 years ago 

Hi David,
	The Comparative Modeling tool isn't ready to handle a mismatched template sequence associated directly onto the target sequence -- particularly if the target sequence has deletions relative to the template sequence.  For now, you need to use an actual alignment of the target sequence with the structure sequence.  I have attached an alignment file with both the target and template sequences in it.  You would open the alignment file in ChimeraX and then 6opc.  Chains A-F will auto-associate with the second (template) alignment sequence.  Chain G, which consists of a bunch of UNK residues, will also spuriously associate (with the target sequence).  You should manually disassociate it or delete it.  Then you will be able to run the comparative modeling.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

realigned.afasta​

by Eric Pettersen, 5 years ago

Attachment: realigned.afasta​ added

Added by email2trac

comment:3 by Eric Pettersen, 5 years ago

Priority: normal → moderate
Summary: Modeller: sequence mismatch to structure → Modeller: cannot handle direction association onto target if deletions in target
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