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Opened 4 months ago
Closed 3 months ago
#18083 closed defect (fixed)
Modeller mismatch failure
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.6-arm64-arm-64bit
ChimeraX Version: 1.11.dev202506232245 (2025-06-23 22:45:56 UTC)
Description
Opened PDB ID 5ttu through the command line, selected K830 and G834 and tried to model the missing loop in between (Model active sequence-viewer region". I got an error, but couldn't report a bug. The same happened if I first downloaded the 5ttu pdb file. If I then used the fasta file, I got the "Report a Bug" possibility.
Log:
UCSF ChimeraX version: 1.11.dev202506232245 (2025-06-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5ttu
5ttu title:
Jak3 with covalent inhibitor 7 [more info...]
Chain information for 5ttu #1
---
Chain | Description | UniProt
A | Tyrosine-protein kinase JAK3 | JAK3_HUMAN 812-1124
Non-standard residues in 5ttu #1
---
7KV —
1-[(3aR,7aR)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)octahydro-6H-pyrrolo[2,3-c]pyridin-6-yl]propan-1-one
SO4 — sulfate ion
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:830
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:830
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:830-834
13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected
> ui tool show "Model Loops"
> modeller refine 1/A:1:27,31 numModels 5 fast false adjacentFlexible 1
> protocol DOPE-HR
Webservices job id: 89L9OVRF3DWYNFC8
Webservices job finished: 89L9OVRF3DWYNFC8
Modeller job (ID 89L9OVRF3DWYNFC8) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 95, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 624, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 577, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 215, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 224, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.6, 2024/10/17, r12888
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 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 crick.cgl.ucsf.edu
4.18.0-553.56.1.el8_10.x86_64 x86_64
Date and time of compilation : 2024/10/17 20:43:03
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2025/06/26 05:07:27
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
dopehr_loo_W> The class 'dopehr_loopmodel' is deprecated; use
'DOPEHRLoopModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528709 516.317
0.504
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 775109 756.942
0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778205 759.966 0.742
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 780217 761.931 0.744
read_al_374_> Non-standard residue type,position,sequence: . 776 1
read_al_374_> Non-standard residue type,position,sequence: . 777 1
read_al_374_> Non-standard residue type,position,sequence: . 778 1
read_al_374_> Non-standard residue type,position,sequence: w 779 1
read_al_374_> Non-standard residue type,position,sequence: w 780 1
read_al_374_> Non-standard residue type,position,sequence: w 781 1
read_al_374_> Non-standard residue type,position,sequence: w 782 1
read_al_374_> Non-standard residue type,position,sequence: w 783 1
read_al_374_> Non-standard residue type,position,sequence: w 784 1
read_al_374_> Non-standard residue type,position,sequence: w 785 1
read_al_374_> Non-standard residue type,position,sequence: w 786 1
read_al_374_> Non-standard residue type,position,sequence: w 787 1
read_al_374_> Non-standard residue type,position,sequence: w 788 1
read_al_374_> Non-standard residue type,position,sequence: w 789 1
read_al_374_> Non-standard residue type,position,sequence: w 790 1
read_al_374_> Non-standard residue type,position,sequence: w 791 1
read_al_374_> Non-standard residue type,position,sequence: w 792 1
read_al_374_> Non-standard residue type,position,sequence: w 793 1
read_al_374_> Non-standard residue type,position,sequence: w 794 1
read_al_374_> Non-standard residue type,position,sequence: w 795 1
read_al_374_> Non-standard residue type,position,sequence: w 796 1
read_al_374_> Non-standard residue type,position,sequence: w 797 1
read_al_374_> Non-standard residue type,position,sequence: w 798 1
read_al_374_> Non-standard residue type,position,sequence: w 799 1
read_al_374_> Non-standard residue type,position,sequence: w 800 1
read_al_374_> Non-standard residue type,position,sequence: w 801 1
read_al_374_> Non-standard residue type,position,sequence: w 802 1
read_al_374_> Non-standard residue type,position,sequence: w 803 1
read_al_374_> Non-standard residue type,position,sequence: w 804 1
read_al_374_> Non-standard residue type,position,sequence: w 805 1
read_al_374_> Non-standard residue type,position,sequence: w 806 1
read_al_374_> Non-standard residue type,position,sequence: w 807 1
read_al_374_> Non-standard residue type,position,sequence: w 808 1
read_al_374_> Non-standard residue type,position,sequence: w 809 1
read_al_374_> Non-standard residue type,position,sequence: w 810 1
read_al_374_> Non-standard residue type,position,sequence: w 811 1
read_al_374_> Non-standard residue type,position,sequence: w 812 1
read_al_374_> Non-standard residue type,position,sequence: w 813 1
read_al_374_> Non-standard residue type,position,sequence: w 814 1
read_al_374_> Non-standard residue type,position,sequence: w 815 1
read_al_374_> Non-standard residue type,position,sequence: w 816 1
read_al_374_> Non-standard residue type,position,sequence: w 817 1
read_al_374_> Non-standard residue type,position,sequence: w 818 1
read_al_374_> Non-standard residue type,position,sequence: w 819 1
read_al_374_> Non-standard residue type,position,sequence: w 820 1
read_al_374_> Non-standard residue type,position,sequence: w 821 1
read_al_374_> Non-standard residue type,position,sequence: w 822 1
read_al_374_> Non-standard residue type,position,sequence: w 823 1
read_al_374_> Non-standard residue type,position,sequence: w 824 1
read_al_374_> Non-standard residue type,position,sequence: w 825 1
read_al_374_> Non-standard residue type,position,sequence: w 826 1
read_al_374_> Non-standard residue type,position,sequence: w 827 1
read_al_374_> Non-standard residue type,position,sequence: w 828 1
read_al_374_> Non-standard residue type,position,sequence: w 829 1
read_al_374_> Non-standard residue type,position,sequence: w 830 1
read_al_374_> Non-standard residue type,position,sequence: w 831 1
read_al_374_> Non-standard residue type,position,sequence: w 832 1
read_al_374_> Non-standard residue type,position,sequence: w 833 1
read_al_374_> Non-standard residue type,position,sequence: w 834 1
read_al_374_> Non-standard residue type,position,sequence: w 835 1
read_al_374_> Non-standard residue type,position,sequence: w 836 1
read_al_374_> Non-standard residue type,position,sequence: w 837 1
read_al_374_> Non-standard residue type,position,sequence: w 838 1
read_al_374_> Non-standard residue type,position,sequence: w 839 1
read_al_374_> Non-standard residue type,position,sequence: w 840 1
read_al_374_> Non-standard residue type,position,sequence: w 841 1
read_al_374_> Non-standard residue type,position,sequence: w 842 1
read_al_374_> Non-standard residue type,position,sequence: w 843 1
read_al_374_> Non-standard residue type,position,sequence: w 844 1
read_al_374_> Non-standard residue type,position,sequence: w 845 1
read_al_374_> Non-standard residue type,position,sequence: w 846 1
read_al_374_> Non-standard residue type,position,sequence: w 847 1
read_al_374_> Non-standard residue type,position,sequence: w 848 1
read_al_374_> Non-standard residue type,position,sequence: w 849 1
read_al_374_> Non-standard residue type,position,sequence: w 850 1
read_al_374_> Non-standard residue type,position,sequence: w 851 1
read_al_374_> Non-standard residue type,position,sequence: w 852 1
read_al_374_> Non-standard residue type,position,sequence: w 853 1
read_al_374_> Non-standard residue type,position,sequence: w 854 1
read_al_374_> Non-standard residue type,position,sequence: w 855 1
read_al_374_> Non-standard residue type,position,sequence: w 856 1
read_al_374_> Non-standard residue type,position,sequence: w 857 1
read_al_374_> Non-standard residue type,position,sequence: w 858 1
read_al_374_> Non-standard residue type,position,sequence: w 859 1
read_al_374_> Non-standard residue type,position,sequence: w 860 1
read_al_374_> Non-standard residue type,position,sequence: w 861 1
read_al_374_> Non-standard residue type,position,sequence: w 862 1
read_al_374_> Non-standard residue type,position,sequence: w 863 1
read_al_374_> Non-standard residue type,position,sequence: w 864 1
read_al_374_> Non-standard residue type,position,sequence: w 865 1
read_al_374_> Non-standard residue type,position,sequence: w 866 1
read_al_374_> Non-standard residue type,position,sequence: w 867 1
read_al_374_> Non-standard residue type,position,sequence: w 868 1
read_al_374_> Non-standard residue type,position,sequence: w 869 1
read_al_374_> Non-standard residue type,position,sequence: w 870 1
read_al_374_> Non-standard residue type,position,sequence: w 871 1
read_al_374_> Non-standard residue type,position,sequence: w 872 1
read_al_374_> Non-standard residue type,position,sequence: w 873 1
read_al_374_> Non-standard residue type,position,sequence: w 874 1
read_al_374_> Non-standard residue type,position,sequence: w 875 1
read_al_374_> Non-standard residue type,position,sequence: w 876 1
read_al_374_> Non-standard residue type,position,sequence: w 877 1
read_al_374_> Non-standard residue type,position,sequence: w 878 1
read_al_374_> Non-standard residue type,position,sequence: w 879 1
read_al_374_> Non-standard residue type,position,sequence: w 880 1
read_al_374_> Non-standard residue type,position,sequence: w 881 1
read_al_374_> Non-standard residue type,position,sequence: w 882 1
read_al_374_> Non-standard residue type,position,sequence: w 883 1
read_al_374_> Non-standard residue type,position,sequence: w 884 1
read_al_374_> Non-standard residue type,position,sequence: w 885 1
read_al_374_> Non-standard residue type,position,sequence: w 886 1
read_al_374_> Non-standard residue type,position,sequence: w 887 1
read_al_374_> Non-standard residue type,position,sequence: w 888 1
read_al_374_> Non-standard residue type,position,sequence: w 889 1
read_al_374_> Non-standard residue type,position,sequence: w 890 1
read_al_374_> Non-standard residue type,position,sequence: w 891 1
read_al_374_> Non-standard residue type,position,sequence: w 892 1
read_al_374_> Non-standard residue type,position,sequence: w 893 1
read_al_374_> Non-standard residue type,position,sequence: w 894 1
read_al_374_> Non-standard residue type,position,sequence: w 895 1
read_al_374_> Non-standard residue type,position,sequence: w 896 1
read_al_374_> Non-standard residue type,position,sequence: w 897 1
read_al_374_> Non-standard residue type,position,sequence: w 898 1
read_al_374_> Non-standard residue type,position,sequence: w 899 1
read_al_374_> Non-standard residue type,position,sequence: w 900 1
read_al_374_> Non-standard residue type,position,sequence: w 901 1
read_al_374_> Non-standard residue type,position,sequence: w 902 1
read_al_374_> Non-standard residue type,position,sequence: w 903 1
read_al_374_> Non-standard residue type,position,sequence: w 904 1
read_al_374_> Non-standard residue type,position,sequence: w 905 1
read_al_374_> Non-standard residue type,position,sequence: w 906 1
read_al_374_> Non-standard residue type,position,sequence: w 907 1
read_al_374_> Non-standard residue type,position,sequence: w 908 1
read_al_374_> Non-standard residue type,position,sequence: w 909 1
read_al_374_> Non-standard residue type,position,sequence: w 910 1
read_al_374_> Non-standard residue type,position,sequence: w 911 1
read_al_374_> Non-standard residue type,position,sequence: w 912 1
read_al_374_> Non-standard residue type,position,sequence: w 913 1
read_al_374_> Non-standard residue type,position,sequence: w 914 1
read_al_374_> Non-standard residue type,position,sequence: w 915 1
read_al_374_> Non-standard residue type,position,sequence: w 916 1
read_al_374_> Non-standard residue type,position,sequence: w 917 1
read_al_374_> Non-standard residue type,position,sequence: w 918 1
read_al_374_> Non-standard residue type,position,sequence: w 919 1
read_al_374_> Non-standard residue type,position,sequence: w 920 1
read_al_374_> Non-standard residue type,position,sequence: w 921 1
read_al_374_> Non-standard residue type,position,sequence: w 922 1
read_al_374_> Non-standard residue type,position,sequence: w 923 1
read_al_374_> Non-standard residue type,position,sequence: w 924 1
read_al_374_> Non-standard residue type,position,sequence: w 925 1
read_al_374_> Non-standard residue type,position,sequence: w 926 1
read_al_374_> Non-standard residue type,position,sequence: w 927 1
read_al_374_> Non-standard residue type,position,sequence: w 928 1
read_al_374_> Non-standard residue type,position,sequence: w 929 1
read_al_374_> Non-standard residue type,position,sequence: w 930 1
read_al_374_> Non-standard residue type,position,sequence: w 931 1
read_al_374_> Non-standard residue type,position,sequence: w 932 1
read_al_374_> Non-standard residue type,position,sequence: w 933 1
read_al_374_> Non-standard residue type,position,sequence: w 934 1
read_al_374_> Non-standard residue type,position,sequence: w 935 1
read_al_374_> Non-standard residue type,position,sequence: w 936 1
read_al_374_> Non-standard residue type,position,sequence: w 937 1
read_al_374_> Non-standard residue type,position,sequence: w 938 1
read_al_374_> Non-standard residue type,position,sequence: w 939 1
read_al_374_> Non-standard residue type,position,sequence: w 940 1
read_al_374_> Non-standard residue type,position,sequence: w 941 1
read_al_374_> Non-standard residue type,position,sequence: w 942 1
read_al_374_> Non-standard residue type,position,sequence: w 943 1
read_al_374_> Non-standard residue type,position,sequence: w 944 1
read_al_374_> Non-standard residue type,position,sequence: w 945 1
read_al_374_> Non-standard residue type,position,sequence: w 946 1
read_al_374_> Non-standard residue type,position,sequence: w 947 1
read_al_374_> Non-standard residue type,position,sequence: w 948 1
read_al_374_> Non-standard residue type,position,sequence: w 949 1
read_al_374_> Non-standard residue type,position,sequence: w 950 1
read_al_374_> Non-standard residue type,position,sequence: w 951 1
read_al_374_> Non-standard residue type,position,sequence: w 952 1
read_al_374_> Non-standard residue type,position,sequence: w 953 1
read_al_374_> Non-standard residue type,position,sequence: w 954 1
read_al_374_> Non-standard residue type,position,sequence: w 955 1
read_al_374_> Non-standard residue type,position,sequence: w 956 1
read_al_374_> Non-standard residue type,position,sequence: w 957 1
read_al_374_> Non-standard residue type,position,sequence: w 958 1
read_al_374_> Non-standard residue type,position,sequence: w 959 1
read_al_374_> Non-standard residue type,position,sequence: w 960 1
read_al_374_> Non-standard residue type,position,sequence: w 961 1
read_al_374_> Non-standard residue type,position,sequence: w 962 1
read_al_374_> Non-standard residue type,position,sequence: w 963 1
read_al_374_> Non-standard residue type,position,sequence: w 964 1
read_al_374_> Non-standard residue type,position,sequence: w 965 1
read_al_374_> Non-standard residue type,position,sequence: w 966 1
read_al_374_> Non-standard residue type,position,sequence: w 967 1
read_al_374_> Non-standard residue type,position,sequence: w 968 1
read_al_374_> Non-standard residue type,position,sequence: w 969 1
read_al_374_> Non-standard residue type,position,sequence: w 970 1
read_al_374_> Non-standard residue type,position,sequence: w 971 1
read_al_374_> Non-standard residue type,position,sequence: w 972 1
read_al_374_> Non-standard residue type,position,sequence: w 973 1
read_al_374_> Non-standard residue type,position,sequence: w 974 1
read_al_374_> Non-standard residue type,position,sequence: w 975 1
read_al_374_> Non-standard residue type,position,sequence: w 976 1
read_al_374_> Non-standard residue type,position,sequence: w 977 1
read_al_374_> Non-standard residue type,position,sequence: w 978 1
read_al_374_> Non-standard residue type,position,sequence: w 979 1
read_al_374_> Non-standard residue type,position,sequence: w 980 1
read_al_374_> Non-standard residue type,position,sequence: w 981 1
read_al_374_> Non-standard residue type,position,sequence: w 982 1
read_al_374_> Non-standard residue type,position,sequence: w 983 1
read_al_374_> Non-standard residue type,position,sequence: w 984 1
read_al_374_> Non-standard residue type,position,sequence: w 985 1
read_al_374_> Non-standard residue type,position,sequence: w 986 1
read_al_374_> Non-standard residue type,position,sequence: w 987 1
read_al_374_> Non-standard residue type,position,sequence: w 988 1
read_al_374_> Non-standard residue type,position,sequence: w 989 1
read_al_374_> Non-standard residue type,position,sequence: w 990 1
read_al_374_> Non-standard residue type,position,sequence: w 991 1
read_al_374_> Non-standard residue type,position,sequence: w 992 1
read_al_374_> Non-standard residue type,position,sequence: w 993 1
read_al_374_> Non-standard residue type,position,sequence: w 994 1
read_al_374_> Non-standard residue type,position,sequence: w 995 1
read_al_374_> Non-standard residue type,position,sequence: w 996 1
read_al_374_> Non-standard residue type,position,sequence: w 997 1
read_al_374_> Non-standard residue type,position,sequence: w 998 1
read_al_374_> Non-standard residue type,position,sequence: w 999 1
read_al_374_> Non-standard residue type,position,sequence: w 1000 1
read_al_374_> Non-standard residue type,position,sequence: w 1001 1
read_al_374_> Non-standard residue type,position,sequence: w 1002 1
read_al_374_> Non-standard residue type,position,sequence: w 1003 1
read_al_374_> Non-standard residue type,position,sequence: w 1004 1
read_al_374_> Non-standard residue type,position,sequence: w 1005 1
read_al_374_> Non-standard residue type,position,sequence: w 1006 1
read_al_374_> Non-standard residue type,position,sequence: w 1007 1
read_al_374_> Non-standard residue type,position,sequence: w 1008 1
read_al_374_> Non-standard residue type,position,sequence: . 272 2
read_al_374_> Non-standard residue type,position,sequence: . 273 2
read_al_374_> Non-standard residue type,position,sequence: . 274 2
read_al_374_> Non-standard residue type,position,sequence: w 275 2
read_al_374_> Non-standard residue type,position,sequence: w 276 2
read_al_374_> Non-standard residue type,position,sequence: w 277 2
read_al_374_> Non-standard residue type,position,sequence: w 278 2
read_al_374_> Non-standard residue type,position,sequence: w 279 2
read_al_374_> Non-standard residue type,position,sequence: w 280 2
read_al_374_> Non-standard residue type,position,sequence: w 281 2
read_al_374_> Non-standard residue type,position,sequence: w 282 2
read_al_374_> Non-standard residue type,position,sequence: w 283 2
read_al_374_> Non-standard residue type,position,sequence: w 284 2
read_al_374_> Non-standard residue type,position,sequence: w 285 2
read_al_374_> Non-standard residue type,position,sequence: w 286 2
read_al_374_> Non-standard residue type,position,sequence: w 287 2
read_al_374_> Non-standard residue type,position,sequence: w 288 2
read_al_374_> Non-standard residue type,position,sequence: w 289 2
read_al_374_> Non-standard residue type,position,sequence: w 290 2
read_al_374_> Non-standard residue type,position,sequence: w 291 2
read_al_374_> Non-standard residue type,position,sequence: w 292 2
read_al_374_> Non-standard residue type,position,sequence: w 293 2
read_al_374_> Non-standard residue type,position,sequence: w 294 2
read_al_374_> Non-standard residue type,position,sequence: w 295 2
read_al_374_> Non-standard residue type,position,sequence: w 296 2
read_al_374_> Non-standard residue type,position,sequence: w 297 2
read_al_374_> Non-standard residue type,position,sequence: w 298 2
read_al_374_> Non-standard residue type,position,sequence: w 299 2
read_al_374_> Non-standard residue type,position,sequence: w 300 2
read_al_374_> Non-standard residue type,position,sequence: w 301 2
read_al_374_> Non-standard residue type,position,sequence: w 302 2
read_al_374_> Non-standard residue type,position,sequence: w 303 2
read_al_374_> Non-standard residue type,position,sequence: w 304 2
read_al_374_> Non-standard residue type,position,sequence: w 305 2
read_al_374_> Non-standard residue type,position,sequence: w 306 2
read_al_374_> Non-standard residue type,position,sequence: w 307 2
read_al_374_> Non-standard residue type,position,sequence: w 308 2
read_al_374_> Non-standard residue type,position,sequence: w 309 2
read_al_374_> Non-standard residue type,position,sequence: w 310 2
read_al_374_> Non-standard residue type,position,sequence: w 311 2
read_al_374_> Non-standard residue type,position,sequence: w 312 2
read_al_374_> Non-standard residue type,position,sequence: w 313 2
read_al_374_> Non-standard residue type,position,sequence: w 314 2
read_al_374_> Non-standard residue type,position,sequence: w 315 2
read_al_374_> Non-standard residue type,position,sequence: w 316 2
read_al_374_> Non-standard residue type,position,sequence: w 317 2
read_al_374_> Non-standard residue type,position,sequence: w 318 2
read_al_374_> Non-standard residue type,position,sequence: w 319 2
read_al_374_> Non-standard residue type,position,sequence: w 320 2
read_al_374_> Non-standard residue type,position,sequence: w 321 2
read_al_374_> Non-standard residue type,position,sequence: w 322 2
read_al_374_> Non-standard residue type,position,sequence: w 323 2
read_al_374_> Non-standard residue type,position,sequence: w 324 2
read_al_374_> Non-standard residue type,position,sequence: w 325 2
read_al_374_> Non-standard residue type,position,sequence: w 326 2
read_al_374_> Non-standard residue type,position,sequence: w 327 2
read_al_374_> Non-standard residue type,position,sequence: w 328 2
read_al_374_> Non-standard residue type,position,sequence: w 329 2
read_al_374_> Non-standard residue type,position,sequence: w 330 2
read_al_374_> Non-standard residue type,position,sequence: w 331 2
read_al_374_> Non-standard residue type,position,sequence: w 332 2
read_al_374_> Non-standard residue type,position,sequence: w 333 2
read_al_374_> Non-standard residue type,position,sequence: w 334 2
read_al_374_> Non-standard residue type,position,sequence: w 335 2
read_al_374_> Non-standard residue type,position,sequence: w 336 2
read_al_374_> Non-standard residue type,position,sequence: w 337 2
read_al_374_> Non-standard residue type,position,sequence: w 338 2
read_al_374_> Non-standard residue type,position,sequence: w 339 2
read_al_374_> Non-standard residue type,position,sequence: w 340 2
read_al_374_> Non-standard residue type,position,sequence: w 341 2
read_al_374_> Non-standard residue type,position,sequence: w 342 2
read_al_374_> Non-standard residue type,position,sequence: w 343 2
read_al_374_> Non-standard residue type,position,sequence: w 344 2
read_al_374_> Non-standard residue type,position,sequence: w 345 2
read_al_374_> Non-standard residue type,position,sequence: w 346 2
read_al_374_> Non-standard residue type,position,sequence: w 347 2
read_al_374_> Non-standard residue type,position,sequence: w 348 2
read_al_374_> Non-standard residue type,position,sequence: w 349 2
read_al_374_> Non-standard residue type,position,sequence: w 350 2
read_al_374_> Non-standard residue type,position,sequence: w 351 2
read_al_374_> Non-standard residue type,position,sequence: w 352 2
read_al_374_> Non-standard residue type,position,sequence: w 353 2
read_al_374_> Non-standard residue type,position,sequence: w 354 2
read_al_374_> Non-standard residue type,position,sequence: w 355 2
read_al_374_> Non-standard residue type,position,sequence: w 356 2
read_al_374_> Non-standard residue type,position,sequence: w 357 2
read_al_374_> Non-standard residue type,position,sequence: w 358 2
read_al_374_> Non-standard residue type,position,sequence: w 359 2
read_al_374_> Non-standard residue type,position,sequence: w 360 2
read_al_374_> Non-standard residue type,position,sequence: w 361 2
read_al_374_> Non-standard residue type,position,sequence: w 362 2
read_al_374_> Non-standard residue type,position,sequence: w 363 2
read_al_374_> Non-standard residue type,position,sequence: w 364 2
read_al_374_> Non-standard residue type,position,sequence: w 365 2
read_al_374_> Non-standard residue type,position,sequence: w 366 2
read_al_374_> Non-standard residue type,position,sequence: w 367 2
read_al_374_> Non-standard residue type,position,sequence: w 368 2
read_al_374_> Non-standard residue type,position,sequence: w 369 2
read_al_374_> Non-standard residue type,position,sequence: w 370 2
read_al_374_> Non-standard residue type,position,sequence: w 371 2
read_al_374_> Non-standard residue type,position,sequence: w 372 2
read_al_374_> Non-standard residue type,position,sequence: w 373 2
read_al_374_> Non-standard residue type,position,sequence: w 374 2
read_al_374_> Non-standard residue type,position,sequence: w 375 2
read_al_374_> Non-standard residue type,position,sequence: w 376 2
read_al_374_> Non-standard residue type,position,sequence: w 377 2
read_al_374_> Non-standard residue type,position,sequence: w 378 2
read_al_374_> Non-standard residue type,position,sequence: w 379 2
read_al_374_> Non-standard residue type,position,sequence: w 380 2
read_al_374_> Non-standard residue type,position,sequence: w 381 2
read_al_374_> Non-standard residue type,position,sequence: w 382 2
read_al_374_> Non-standard residue type,position,sequence: w 383 2
read_al_374_> Non-standard residue type,position,sequence: w 384 2
read_al_374_> Non-standard residue type,position,sequence: w 385 2
read_al_374_> Non-standard residue type,position,sequence: w 386 2
read_al_374_> Non-standard residue type,position,sequence: w 387 2
read_al_374_> Non-standard residue type,position,sequence: w 388 2
read_al_374_> Non-standard residue type,position,sequence: w 389 2
read_al_374_> Non-standard residue type,position,sequence: w 390 2
read_al_374_> Non-standard residue type,position,sequence: w 391 2
read_al_374_> Non-standard residue type,position,sequence: w 392 2
read_al_374_> Non-standard residue type,position,sequence: w 393 2
read_al_374_> Non-standard residue type,position,sequence: w 394 2
read_al_374_> Non-standard residue type,position,sequence: w 395 2
read_al_374_> Non-standard residue type,position,sequence: w 396 2
read_al_374_> Non-standard residue type,position,sequence: w 397 2
read_al_374_> Non-standard residue type,position,sequence: w 398 2
read_al_374_> Non-standard residue type,position,sequence: w 399 2
read_al_374_> Non-standard residue type,position,sequence: w 400 2
read_al_374_> Non-standard residue type,position,sequence: w 401 2
read_al_374_> Non-standard residue type,position,sequence: w 402 2
read_al_374_> Non-standard residue type,position,sequence: w 403 2
read_al_374_> Non-standard residue type,position,sequence: w 404 2
read_al_374_> Non-standard residue type,position,sequence: w 405 2
read_al_374_> Non-standard residue type,position,sequence: w 406 2
read_al_374_> Non-standard residue type,position,sequence: w 407 2
read_al_374_> Non-standard residue type,position,sequence: w 408 2
read_al_374_> Non-standard residue type,position,sequence: w 409 2
read_al_374_> Non-standard residue type,position,sequence: w 410 2
read_al_374_> Non-standard residue type,position,sequence: w 411 2
read_al_374_> Non-standard residue type,position,sequence: w 412 2
read_al_374_> Non-standard residue type,position,sequence: w 413 2
read_al_374_> Non-standard residue type,position,sequence: w 414 2
read_al_374_> Non-standard residue type,position,sequence: w 415 2
read_al_374_> Non-standard residue type,position,sequence: w 416 2
read_al_374_> Non-standard residue type,position,sequence: w 417 2
read_al_374_> Non-standard residue type,position,sequence: w 418 2
read_al_374_> Non-standard residue type,position,sequence: w 419 2
read_al_374_> Non-standard residue type,position,sequence: w 420 2
read_al_374_> Non-standard residue type,position,sequence: w 421 2
read_al_374_> Non-standard residue type,position,sequence: w 422 2
read_al_374_> Non-standard residue type,position,sequence: w 423 2
read_al_374_> Non-standard residue type,position,sequence: w 424 2
read_al_374_> Non-standard residue type,position,sequence: w 425 2
read_al_374_> Non-standard residue type,position,sequence: w 426 2
read_al_374_> Non-standard residue type,position,sequence: w 427 2
read_al_374_> Non-standard residue type,position,sequence: w 428 2
read_al_374_> Non-standard residue type,position,sequence: w 429 2
read_al_374_> Non-standard residue type,position,sequence: w 430 2
read_al_374_> Non-standard residue type,position,sequence: w 431 2
read_al_374_> Non-standard residue type,position,sequence: w 432 2
read_al_374_> Non-standard residue type,position,sequence: w 433 2
read_al_374_> Non-standard residue type,position,sequence: w 434 2
read_al_374_> Non-standard residue type,position,sequence: w 435 2
read_al_374_> Non-standard residue type,position,sequence: w 436 2
read_al_374_> Non-standard residue type,position,sequence: w 437 2
read_al_374_> Non-standard residue type,position,sequence: w 438 2
read_al_374_> Non-standard residue type,position,sequence: w 439 2
read_al_374_> Non-standard residue type,position,sequence: w 440 2
read_al_374_> Non-standard residue type,position,sequence: w 441 2
read_al_374_> Non-standard residue type,position,sequence: w 442 2
read_al_374_> Non-standard residue type,position,sequence: w 443 2
read_al_374_> Non-standard residue type,position,sequence: w 444 2
read_al_374_> Non-standard residue type,position,sequence: w 445 2
read_al_374_> Non-standard residue type,position,sequence: w 446 2
read_al_374_> Non-standard residue type,position,sequence: w 447 2
read_al_374_> Non-standard residue type,position,sequence: w 448 2
read_al_374_> Non-standard residue type,position,sequence: w 449 2
read_al_374_> Non-standard residue type,position,sequence: w 450 2
read_al_374_> Non-standard residue type,position,sequence: w 451 2
read_al_374_> Non-standard residue type,position,sequence: w 452 2
read_al_374_> Non-standard residue type,position,sequence: w 453 2
read_al_374_> Non-standard residue type,position,sequence: w 454 2
read_al_374_> Non-standard residue type,position,sequence: w 455 2
read_al_374_> Non-standard residue type,position,sequence: w 456 2
read_al_374_> Non-standard residue type,position,sequence: w 457 2
read_al_374_> Non-standard residue type,position,sequence: w 458 2
read_al_374_> Non-standard residue type,position,sequence: w 459 2
read_al_374_> Non-standard residue type,position,sequence: w 460 2
read_al_374_> Non-standard residue type,position,sequence: w 461 2
read_al_374_> Non-standard residue type,position,sequence: w 462 2
read_al_374_> Non-standard residue type,position,sequence: w 463 2
read_al_374_> Non-standard residue type,position,sequence: w 464 2
read_al_374_> Non-standard residue type,position,sequence: w 465 2
read_al_374_> Non-standard residue type,position,sequence: w 466 2
read_al_374_> Non-standard residue type,position,sequence: w 467 2
read_al_374_> Non-standard residue type,position,sequence: w 468 2
read_al_374_> Non-standard residue type,position,sequence: w 469 2
read_al_374_> Non-standard residue type,position,sequence: w 470 2
read_al_374_> Non-standard residue type,position,sequence: w 471 2
read_al_374_> Non-standard residue type,position,sequence: w 472 2
read_al_374_> Non-standard residue type,position,sequence: w 473 2
read_al_374_> Non-standard residue type,position,sequence: w 474 2
read_al_374_> Non-standard residue type,position,sequence: w 475 2
read_al_374_> Non-standard residue type,position,sequence: w 476 2
read_al_374_> Non-standard residue type,position,sequence: w 477 2
read_al_374_> Non-standard residue type,position,sequence: w 478 2
read_al_374_> Non-standard residue type,position,sequence: w 479 2
read_al_374_> Non-standard residue type,position,sequence: w 480 2
read_al_374_> Non-standard residue type,position,sequence: w 481 2
read_al_374_> Non-standard residue type,position,sequence: w 482 2
read_al_374_> Non-standard residue type,position,sequence: w 483 2
read_al_374_> Non-standard residue type,position,sequence: w 484 2
read_al_374_> Non-standard residue type,position,sequence: w 485 2
read_al_374_> Non-standard residue type,position,sequence: w 486 2
read_al_374_> Non-standard residue type,position,sequence: w 487 2
read_al_374_> Non-standard residue type,position,sequence: w 488 2
read_al_374_> Non-standard residue type,position,sequence: w 489 2
read_al_374_> Non-standard residue type,position,sequence: w 490 2
read_al_374_> Non-standard residue type,position,sequence: w 491 2
read_al_374_> Non-standard residue type,position,sequence: w 492 2
read_al_374_> Non-standard residue type,position,sequence: w 493 2
read_al_374_> Non-standard residue type,position,sequence: w 494 2
read_al_374_> Non-standard residue type,position,sequence: w 495 2
read_al_374_> Non-standard residue type,position,sequence: w 496 2
read_al_374_> Non-standard residue type,position,sequence: w 497 2
read_al_374_> Non-standard residue type,position,sequence: w 498 2
read_al_374_> Non-standard residue type,position,sequence: w 499 2
read_al_374_> Non-standard residue type,position,sequence: w 500 2
read_al_374_> Non-standard residue type,position,sequence: w 501 2
read_al_374_> Non-standard residue type,position,sequence: w 502 2
read_al_374_> Non-standard residue type,position,sequence: w 503 2
read_al_374_> Non-standard residue type,position,sequence: w 504 2
Read the alignment from file : alignment.ali
Total number of alignment positions: 1008
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5ttu_1 775 1 5ttu_1
2 chain_A 504 1 chain_A
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5ttu_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1014442 990.666
0.967
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1014442 990.666
0.967
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1014613 990.833
0.968
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1015463 991.663
0.968
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1016721 992.892
0.970
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1018625 994.751
0.971
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1018625 994.751
0.971
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1018715 994.839
0.972
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1021571 997.628
0.974
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1021571 997.628
0.974
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1021706 997.760
0.974
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1025990 1001.943
0.978
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1025990 1001.943
0.978
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1026188 1002.137
0.979
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1032614 1008.412
0.985
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1032614 1008.412
0.985
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1032911 1008.702
0.985
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1042533 1018.099
0.994
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1042533 1018.099
0.994
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1042983 1018.538
0.995
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1057433 1032.649
1.008
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1057433 1032.649
1.008
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1058108 1033.309
1.009
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1079766 1054.459
1.030
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1079766 1054.459
1.030
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1080774 1055.443
1.031
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1113278 1087.186
1.062
read_pd_459W> Residue type 7KV not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type SO4 not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1113278 1087.186
1.062
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1114790 1088.662
1.063
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1117220 1091.035
1.065
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 272)
Alignment LDMLWTIFEERHLKYISQLGKGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREI
PDB LDMLW...wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
Match *****
Alignment residue type 17 (T, THR) does not match pdb
residue type 67 (., 7KV),
for align code 5ttu_1 (atom file 5ttu_1), pdb residue number " 1201", chain
"A"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5ttu_1
No output models from Modeller; see log for Modeller text output.
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module1/Exercise/5ttu.pdb
5ttu.pdb title:
JAK3 with covalent inhibitor 7 [more info...]
Chain information for 5ttu.pdb #2
---
Chain | Description | UniProt
A | tyrosine-protein kinase JAK3 | JAK3_HUMAN 812-1124
Non-standard residues in 5ttu.pdb #2
---
7KV —
1-[(3AR,7AR)-1-(7H-pyrrolo[2,3-D]pyrimidin-4-yl)octahydro-6H-pyrrolo[2,3-C]pyridin-6-yl]propan-1-one
SO4 — sulfate ion
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #1
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
> select /A:830
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:830
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:830-834
13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected
> ui tool show "Model Loops"
> modeller refine 2/A:1:27,31 numModels 5 fast false adjacentFlexible 1
> protocol DOPE-HR
Webservices job id: XEHZW3DY4L16IZBR
Webservices job finished: XEHZW3DY4L16IZBR
Modeller job (ID XEHZW3DY4L16IZBR) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 95, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 624, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 577, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 215, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 224, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.6, 2024/10/17, r12888
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 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 crick.cgl.ucsf.edu
4.18.0-553.56.1.el8_10.x86_64 x86_64
Date and time of compilation : 2024/10/17 20:43:03
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2025/06/26 05:08:54
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
dopehr_loo_W> The class 'dopehr_loopmodel' is deprecated; use
'DOPEHRLoopModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528709 516.317
0.504
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 775109 756.942
0.739
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778205 759.966 0.742
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 780217 761.931 0.744
read_al_374_> Non-standard residue type,position,sequence: . 776 1
read_al_374_> Non-standard residue type,position,sequence: . 777 1
read_al_374_> Non-standard residue type,position,sequence: . 778 1
read_al_374_> Non-standard residue type,position,sequence: w 779 1
read_al_374_> Non-standard residue type,position,sequence: w 780 1
read_al_374_> Non-standard residue type,position,sequence: w 781 1
read_al_374_> Non-standard residue type,position,sequence: w 782 1
read_al_374_> Non-standard residue type,position,sequence: w 783 1
read_al_374_> Non-standard residue type,position,sequence: w 784 1
read_al_374_> Non-standard residue type,position,sequence: w 785 1
read_al_374_> Non-standard residue type,position,sequence: w 786 1
read_al_374_> Non-standard residue type,position,sequence: w 787 1
read_al_374_> Non-standard residue type,position,sequence: w 788 1
read_al_374_> Non-standard residue type,position,sequence: w 789 1
read_al_374_> Non-standard residue type,position,sequence: w 790 1
read_al_374_> Non-standard residue type,position,sequence: w 791 1
read_al_374_> Non-standard residue type,position,sequence: w 792 1
read_al_374_> Non-standard residue type,position,sequence: w 793 1
read_al_374_> Non-standard residue type,position,sequence: w 794 1
read_al_374_> Non-standard residue type,position,sequence: w 795 1
read_al_374_> Non-standard residue type,position,sequence: w 796 1
read_al_374_> Non-standard residue type,position,sequence: w 797 1
read_al_374_> Non-standard residue type,position,sequence: w 798 1
read_al_374_> Non-standard residue type,position,sequence: w 799 1
read_al_374_> Non-standard residue type,position,sequence: w 800 1
read_al_374_> Non-standard residue type,position,sequence: w 801 1
read_al_374_> Non-standard residue type,position,sequence: w 802 1
read_al_374_> Non-standard residue type,position,sequence: w 803 1
read_al_374_> Non-standard residue type,position,sequence: w 804 1
read_al_374_> Non-standard residue type,position,sequence: w 805 1
read_al_374_> Non-standard residue type,position,sequence: w 806 1
read_al_374_> Non-standard residue type,position,sequence: w 807 1
read_al_374_> Non-standard residue type,position,sequence: w 808 1
read_al_374_> Non-standard residue type,position,sequence: w 809 1
read_al_374_> Non-standard residue type,position,sequence: w 810 1
read_al_374_> Non-standard residue type,position,sequence: w 811 1
read_al_374_> Non-standard residue type,position,sequence: w 812 1
read_al_374_> Non-standard residue type,position,sequence: w 813 1
read_al_374_> Non-standard residue type,position,sequence: w 814 1
read_al_374_> Non-standard residue type,position,sequence: w 815 1
read_al_374_> Non-standard residue type,position,sequence: w 816 1
read_al_374_> Non-standard residue type,position,sequence: w 817 1
read_al_374_> Non-standard residue type,position,sequence: w 818 1
read_al_374_> Non-standard residue type,position,sequence: w 819 1
read_al_374_> Non-standard residue type,position,sequence: w 820 1
read_al_374_> Non-standard residue type,position,sequence: w 821 1
read_al_374_> Non-standard residue type,position,sequence: w 822 1
read_al_374_> Non-standard residue type,position,sequence: w 823 1
read_al_374_> Non-standard residue type,position,sequence: w 824 1
read_al_374_> Non-standard residue type,position,sequence: w 825 1
read_al_374_> Non-standard residue type,position,sequence: w 826 1
read_al_374_> Non-standard residue type,position,sequence: w 827 1
read_al_374_> Non-standard residue type,position,sequence: w 828 1
read_al_374_> Non-standard residue type,position,sequence: w 829 1
read_al_374_> Non-standard residue type,position,sequence: w 830 1
read_al_374_> Non-standard residue type,position,sequence: w 831 1
read_al_374_> Non-standard residue type,position,sequence: w 832 1
read_al_374_> Non-standard residue type,position,sequence: w 833 1
read_al_374_> Non-standard residue type,position,sequence: w 834 1
read_al_374_> Non-standard residue type,position,sequence: w 835 1
read_al_374_> Non-standard residue type,position,sequence: w 836 1
read_al_374_> Non-standard residue type,position,sequence: w 837 1
read_al_374_> Non-standard residue type,position,sequence: w 838 1
read_al_374_> Non-standard residue type,position,sequence: w 839 1
read_al_374_> Non-standard residue type,position,sequence: w 840 1
read_al_374_> Non-standard residue type,position,sequence: w 841 1
read_al_374_> Non-standard residue type,position,sequence: w 842 1
read_al_374_> Non-standard residue type,position,sequence: w 843 1
read_al_374_> Non-standard residue type,position,sequence: w 844 1
read_al_374_> Non-standard residue type,position,sequence: w 845 1
read_al_374_> Non-standard residue type,position,sequence: w 846 1
read_al_374_> Non-standard residue type,position,sequence: w 847 1
read_al_374_> Non-standard residue type,position,sequence: w 848 1
read_al_374_> Non-standard residue type,position,sequence: w 849 1
read_al_374_> Non-standard residue type,position,sequence: w 850 1
read_al_374_> Non-standard residue type,position,sequence: w 851 1
read_al_374_> Non-standard residue type,position,sequence: w 852 1
read_al_374_> Non-standard residue type,position,sequence: w 853 1
read_al_374_> Non-standard residue type,position,sequence: w 854 1
read_al_374_> Non-standard residue type,position,sequence: w 855 1
read_al_374_> Non-standard residue type,position,sequence: w 856 1
read_al_374_> Non-standard residue type,position,sequence: w 857 1
read_al_374_> Non-standard residue type,position,sequence: w 858 1
read_al_374_> Non-standard residue type,position,sequence: w 859 1
read_al_374_> Non-standard residue type,position,sequence: w 860 1
read_al_374_> Non-standard residue type,position,sequence: w 861 1
read_al_374_> Non-standard residue type,position,sequence: w 862 1
read_al_374_> Non-standard residue type,position,sequence: w 863 1
read_al_374_> Non-standard residue type,position,sequence: w 864 1
read_al_374_> Non-standard residue type,position,sequence: w 865 1
read_al_374_> Non-standard residue type,position,sequence: w 866 1
read_al_374_> Non-standard residue type,position,sequence: w 867 1
read_al_374_> Non-standard residue type,position,sequence: w 868 1
read_al_374_> Non-standard residue type,position,sequence: w 869 1
read_al_374_> Non-standard residue type,position,sequence: w 870 1
read_al_374_> Non-standard residue type,position,sequence: w 871 1
read_al_374_> Non-standard residue type,position,sequence: w 872 1
read_al_374_> Non-standard residue type,position,sequence: w 873 1
read_al_374_> Non-standard residue type,position,sequence: w 874 1
read_al_374_> Non-standard residue type,position,sequence: w 875 1
read_al_374_> Non-standard residue type,position,sequence: w 876 1
read_al_374_> Non-standard residue type,position,sequence: w 877 1
read_al_374_> Non-standard residue type,position,sequence: w 878 1
read_al_374_> Non-standard residue type,position,sequence: w 879 1
read_al_374_> Non-standard residue type,position,sequence: w 880 1
read_al_374_> Non-standard residue type,position,sequence: w 881 1
read_al_374_> Non-standard residue type,position,sequence: w 882 1
read_al_374_> Non-standard residue type,position,sequence: w 883 1
read_al_374_> Non-standard residue type,position,sequence: w 884 1
read_al_374_> Non-standard residue type,position,sequence: w 885 1
read_al_374_> Non-standard residue type,position,sequence: w 886 1
read_al_374_> Non-standard residue type,position,sequence: w 887 1
read_al_374_> Non-standard residue type,position,sequence: w 888 1
read_al_374_> Non-standard residue type,position,sequence: w 889 1
read_al_374_> Non-standard residue type,position,sequence: w 890 1
read_al_374_> Non-standard residue type,position,sequence: w 891 1
read_al_374_> Non-standard residue type,position,sequence: w 892 1
read_al_374_> Non-standard residue type,position,sequence: w 893 1
read_al_374_> Non-standard residue type,position,sequence: w 894 1
read_al_374_> Non-standard residue type,position,sequence: w 895 1
read_al_374_> Non-standard residue type,position,sequence: w 896 1
read_al_374_> Non-standard residue type,position,sequence: w 897 1
read_al_374_> Non-standard residue type,position,sequence: w 898 1
read_al_374_> Non-standard residue type,position,sequence: w 899 1
read_al_374_> Non-standard residue type,position,sequence: w 900 1
read_al_374_> Non-standard residue type,position,sequence: w 901 1
read_al_374_> Non-standard residue type,position,sequence: w 902 1
read_al_374_> Non-standard residue type,position,sequence: w 903 1
read_al_374_> Non-standard residue type,position,sequence: w 904 1
read_al_374_> Non-standard residue type,position,sequence: w 905 1
read_al_374_> Non-standard residue type,position,sequence: w 906 1
read_al_374_> Non-standard residue type,position,sequence: w 907 1
read_al_374_> Non-standard residue type,position,sequence: w 908 1
read_al_374_> Non-standard residue type,position,sequence: w 909 1
read_al_374_> Non-standard residue type,position,sequence: w 910 1
read_al_374_> Non-standard residue type,position,sequence: w 911 1
read_al_374_> Non-standard residue type,position,sequence: w 912 1
read_al_374_> Non-standard residue type,position,sequence: w 913 1
read_al_374_> Non-standard residue type,position,sequence: w 914 1
read_al_374_> Non-standard residue type,position,sequence: w 915 1
read_al_374_> Non-standard residue type,position,sequence: w 916 1
read_al_374_> Non-standard residue type,position,sequence: w 917 1
read_al_374_> Non-standard residue type,position,sequence: w 918 1
read_al_374_> Non-standard residue type,position,sequence: w 919 1
read_al_374_> Non-standard residue type,position,sequence: w 920 1
read_al_374_> Non-standard residue type,position,sequence: w 921 1
read_al_374_> Non-standard residue type,position,sequence: w 922 1
read_al_374_> Non-standard residue type,position,sequence: w 923 1
read_al_374_> Non-standard residue type,position,sequence: w 924 1
read_al_374_> Non-standard residue type,position,sequence: w 925 1
read_al_374_> Non-standard residue type,position,sequence: w 926 1
read_al_374_> Non-standard residue type,position,sequence: w 927 1
read_al_374_> Non-standard residue type,position,sequence: w 928 1
read_al_374_> Non-standard residue type,position,sequence: w 929 1
read_al_374_> Non-standard residue type,position,sequence: w 930 1
read_al_374_> Non-standard residue type,position,sequence: w 931 1
read_al_374_> Non-standard residue type,position,sequence: w 932 1
read_al_374_> Non-standard residue type,position,sequence: w 933 1
read_al_374_> Non-standard residue type,position,sequence: w 934 1
read_al_374_> Non-standard residue type,position,sequence: w 935 1
read_al_374_> Non-standard residue type,position,sequence: w 936 1
read_al_374_> Non-standard residue type,position,sequence: w 937 1
read_al_374_> Non-standard residue type,position,sequence: w 938 1
read_al_374_> Non-standard residue type,position,sequence: w 939 1
read_al_374_> Non-standard residue type,position,sequence: w 940 1
read_al_374_> Non-standard residue type,position,sequence: w 941 1
read_al_374_> Non-standard residue type,position,sequence: w 942 1
read_al_374_> Non-standard residue type,position,sequence: w 943 1
read_al_374_> Non-standard residue type,position,sequence: w 944 1
read_al_374_> Non-standard residue type,position,sequence: w 945 1
read_al_374_> Non-standard residue type,position,sequence: w 946 1
read_al_374_> Non-standard residue type,position,sequence: w 947 1
read_al_374_> Non-standard residue type,position,sequence: w 948 1
read_al_374_> Non-standard residue type,position,sequence: w 949 1
read_al_374_> Non-standard residue type,position,sequence: w 950 1
read_al_374_> Non-standard residue type,position,sequence: w 951 1
read_al_374_> Non-standard residue type,position,sequence: w 952 1
read_al_374_> Non-standard residue type,position,sequence: w 953 1
read_al_374_> Non-standard residue type,position,sequence: w 954 1
read_al_374_> Non-standard residue type,position,sequence: w 955 1
read_al_374_> Non-standard residue type,position,sequence: w 956 1
read_al_374_> Non-standard residue type,position,sequence: w 957 1
read_al_374_> Non-standard residue type,position,sequence: w 958 1
read_al_374_> Non-standard residue type,position,sequence: w 959 1
read_al_374_> Non-standard residue type,position,sequence: w 960 1
read_al_374_> Non-standard residue type,position,sequence: w 961 1
read_al_374_> Non-standard residue type,position,sequence: w 962 1
read_al_374_> Non-standard residue type,position,sequence: w 963 1
read_al_374_> Non-standard residue type,position,sequence: w 964 1
read_al_374_> Non-standard residue type,position,sequence: w 965 1
read_al_374_> Non-standard residue type,position,sequence: w 966 1
read_al_374_> Non-standard residue type,position,sequence: w 967 1
read_al_374_> Non-standard residue type,position,sequence: w 968 1
read_al_374_> Non-standard residue type,position,sequence: w 969 1
read_al_374_> Non-standard residue type,position,sequence: w 970 1
read_al_374_> Non-standard residue type,position,sequence: w 971 1
read_al_374_> Non-standard residue type,position,sequence: w 972 1
read_al_374_> Non-standard residue type,position,sequence: w 973 1
read_al_374_> Non-standard residue type,position,sequence: w 974 1
read_al_374_> Non-standard residue type,position,sequence: w 975 1
read_al_374_> Non-standard residue type,position,sequence: w 976 1
read_al_374_> Non-standard residue type,position,sequence: w 977 1
read_al_374_> Non-standard residue type,position,sequence: w 978 1
read_al_374_> Non-standard residue type,position,sequence: w 979 1
read_al_374_> Non-standard residue type,position,sequence: w 980 1
read_al_374_> Non-standard residue type,position,sequence: w 981 1
read_al_374_> Non-standard residue type,position,sequence: w 982 1
read_al_374_> Non-standard residue type,position,sequence: w 983 1
read_al_374_> Non-standard residue type,position,sequence: w 984 1
read_al_374_> Non-standard residue type,position,sequence: w 985 1
read_al_374_> Non-standard residue type,position,sequence: w 986 1
read_al_374_> Non-standard residue type,position,sequence: w 987 1
read_al_374_> Non-standard residue type,position,sequence: w 988 1
read_al_374_> Non-standard residue type,position,sequence: w 989 1
read_al_374_> Non-standard residue type,position,sequence: w 990 1
read_al_374_> Non-standard residue type,position,sequence: w 991 1
read_al_374_> Non-standard residue type,position,sequence: w 992 1
read_al_374_> Non-standard residue type,position,sequence: w 993 1
read_al_374_> Non-standard residue type,position,sequence: w 994 1
read_al_374_> Non-standard residue type,position,sequence: w 995 1
read_al_374_> Non-standard residue type,position,sequence: w 996 1
read_al_374_> Non-standard residue type,position,sequence: w 997 1
read_al_374_> Non-standard residue type,position,sequence: w 998 1
read_al_374_> Non-standard residue type,position,sequence: w 999 1
read_al_374_> Non-standard residue type,position,sequence: w 1000 1
read_al_374_> Non-standard residue type,position,sequence: w 1001 1
read_al_374_> Non-standard residue type,position,sequence: w 1002 1
read_al_374_> Non-standard residue type,position,sequence: w 1003 1
read_al_374_> Non-standard residue type,position,sequence: w 1004 1
read_al_374_> Non-standard residue type,position,sequence: w 1005 1
read_al_374_> Non-standard residue type,position,sequence: w 1006 1
read_al_374_> Non-standard residue type,position,sequence: w 1007 1
read_al_374_> Non-standard residue type,position,sequence: w 1008 1
read_al_374_> Non-standard residue type,position,sequence: . 272 2
read_al_374_> Non-standard residue type,position,sequence: . 273 2
read_al_374_> Non-standard residue type,position,sequence: . 274 2
read_al_374_> Non-standard residue type,position,sequence: w 275 2
read_al_374_> Non-standard residue type,position,sequence: w 276 2
read_al_374_> Non-standard residue type,position,sequence: w 277 2
read_al_374_> Non-standard residue type,position,sequence: w 278 2
read_al_374_> Non-standard residue type,position,sequence: w 279 2
read_al_374_> Non-standard residue type,position,sequence: w 280 2
read_al_374_> Non-standard residue type,position,sequence: w 281 2
read_al_374_> Non-standard residue type,position,sequence: w 282 2
read_al_374_> Non-standard residue type,position,sequence: w 283 2
read_al_374_> Non-standard residue type,position,sequence: w 284 2
read_al_374_> Non-standard residue type,position,sequence: w 285 2
read_al_374_> Non-standard residue type,position,sequence: w 286 2
read_al_374_> Non-standard residue type,position,sequence: w 287 2
read_al_374_> Non-standard residue type,position,sequence: w 288 2
read_al_374_> Non-standard residue type,position,sequence: w 289 2
read_al_374_> Non-standard residue type,position,sequence: w 290 2
read_al_374_> Non-standard residue type,position,sequence: w 291 2
read_al_374_> Non-standard residue type,position,sequence: w 292 2
read_al_374_> Non-standard residue type,position,sequence: w 293 2
read_al_374_> Non-standard residue type,position,sequence: w 294 2
read_al_374_> Non-standard residue type,position,sequence: w 295 2
read_al_374_> Non-standard residue type,position,sequence: w 296 2
read_al_374_> Non-standard residue type,position,sequence: w 297 2
read_al_374_> Non-standard residue type,position,sequence: w 298 2
read_al_374_> Non-standard residue type,position,sequence: w 299 2
read_al_374_> Non-standard residue type,position,sequence: w 300 2
read_al_374_> Non-standard residue type,position,sequence: w 301 2
read_al_374_> Non-standard residue type,position,sequence: w 302 2
read_al_374_> Non-standard residue type,position,sequence: w 303 2
read_al_374_> Non-standard residue type,position,sequence: w 304 2
read_al_374_> Non-standard residue type,position,sequence: w 305 2
read_al_374_> Non-standard residue type,position,sequence: w 306 2
read_al_374_> Non-standard residue type,position,sequence: w 307 2
read_al_374_> Non-standard residue type,position,sequence: w 308 2
read_al_374_> Non-standard residue type,position,sequence: w 309 2
read_al_374_> Non-standard residue type,position,sequence: w 310 2
read_al_374_> Non-standard residue type,position,sequence: w 311 2
read_al_374_> Non-standard residue type,position,sequence: w 312 2
read_al_374_> Non-standard residue type,position,sequence: w 313 2
read_al_374_> Non-standard residue type,position,sequence: w 314 2
read_al_374_> Non-standard residue type,position,sequence: w 315 2
read_al_374_> Non-standard residue type,position,sequence: w 316 2
read_al_374_> Non-standard residue type,position,sequence: w 317 2
read_al_374_> Non-standard residue type,position,sequence: w 318 2
read_al_374_> Non-standard residue type,position,sequence: w 319 2
read_al_374_> Non-standard residue type,position,sequence: w 320 2
read_al_374_> Non-standard residue type,position,sequence: w 321 2
read_al_374_> Non-standard residue type,position,sequence: w 322 2
read_al_374_> Non-standard residue type,position,sequence: w 323 2
read_al_374_> Non-standard residue type,position,sequence: w 324 2
read_al_374_> Non-standard residue type,position,sequence: w 325 2
read_al_374_> Non-standard residue type,position,sequence: w 326 2
read_al_374_> Non-standard residue type,position,sequence: w 327 2
read_al_374_> Non-standard residue type,position,sequence: w 328 2
read_al_374_> Non-standard residue type,position,sequence: w 329 2
read_al_374_> Non-standard residue type,position,sequence: w 330 2
read_al_374_> Non-standard residue type,position,sequence: w 331 2
read_al_374_> Non-standard residue type,position,sequence: w 332 2
read_al_374_> Non-standard residue type,position,sequence: w 333 2
read_al_374_> Non-standard residue type,position,sequence: w 334 2
read_al_374_> Non-standard residue type,position,sequence: w 335 2
read_al_374_> Non-standard residue type,position,sequence: w 336 2
read_al_374_> Non-standard residue type,position,sequence: w 337 2
read_al_374_> Non-standard residue type,position,sequence: w 338 2
read_al_374_> Non-standard residue type,position,sequence: w 339 2
read_al_374_> Non-standard residue type,position,sequence: w 340 2
read_al_374_> Non-standard residue type,position,sequence: w 341 2
read_al_374_> Non-standard residue type,position,sequence: w 342 2
read_al_374_> Non-standard residue type,position,sequence: w 343 2
read_al_374_> Non-standard residue type,position,sequence: w 344 2
read_al_374_> Non-standard residue type,position,sequence: w 345 2
read_al_374_> Non-standard residue type,position,sequence: w 346 2
read_al_374_> Non-standard residue type,position,sequence: w 347 2
read_al_374_> Non-standard residue type,position,sequence: w 348 2
read_al_374_> Non-standard residue type,position,sequence: w 349 2
read_al_374_> Non-standard residue type,position,sequence: w 350 2
read_al_374_> Non-standard residue type,position,sequence: w 351 2
read_al_374_> Non-standard residue type,position,sequence: w 352 2
read_al_374_> Non-standard residue type,position,sequence: w 353 2
read_al_374_> Non-standard residue type,position,sequence: w 354 2
read_al_374_> Non-standard residue type,position,sequence: w 355 2
read_al_374_> Non-standard residue type,position,sequence: w 356 2
read_al_374_> Non-standard residue type,position,sequence: w 357 2
read_al_374_> Non-standard residue type,position,sequence: w 358 2
read_al_374_> Non-standard residue type,position,sequence: w 359 2
read_al_374_> Non-standard residue type,position,sequence: w 360 2
read_al_374_> Non-standard residue type,position,sequence: w 361 2
read_al_374_> Non-standard residue type,position,sequence: w 362 2
read_al_374_> Non-standard residue type,position,sequence: w 363 2
read_al_374_> Non-standard residue type,position,sequence: w 364 2
read_al_374_> Non-standard residue type,position,sequence: w 365 2
read_al_374_> Non-standard residue type,position,sequence: w 366 2
read_al_374_> Non-standard residue type,position,sequence: w 367 2
read_al_374_> Non-standard residue type,position,sequence: w 368 2
read_al_374_> Non-standard residue type,position,sequence: w 369 2
read_al_374_> Non-standard residue type,position,sequence: w 370 2
read_al_374_> Non-standard residue type,position,sequence: w 371 2
read_al_374_> Non-standard residue type,position,sequence: w 372 2
read_al_374_> Non-standard residue type,position,sequence: w 373 2
read_al_374_> Non-standard residue type,position,sequence: w 374 2
read_al_374_> Non-standard residue type,position,sequence: w 375 2
read_al_374_> Non-standard residue type,position,sequence: w 376 2
read_al_374_> Non-standard residue type,position,sequence: w 377 2
read_al_374_> Non-standard residue type,position,sequence: w 378 2
read_al_374_> Non-standard residue type,position,sequence: w 379 2
read_al_374_> Non-standard residue type,position,sequence: w 380 2
read_al_374_> Non-standard residue type,position,sequence: w 381 2
read_al_374_> Non-standard residue type,position,sequence: w 382 2
read_al_374_> Non-standard residue type,position,sequence: w 383 2
read_al_374_> Non-standard residue type,position,sequence: w 384 2
read_al_374_> Non-standard residue type,position,sequence: w 385 2
read_al_374_> Non-standard residue type,position,sequence: w 386 2
read_al_374_> Non-standard residue type,position,sequence: w 387 2
read_al_374_> Non-standard residue type,position,sequence: w 388 2
read_al_374_> Non-standard residue type,position,sequence: w 389 2
read_al_374_> Non-standard residue type,position,sequence: w 390 2
read_al_374_> Non-standard residue type,position,sequence: w 391 2
read_al_374_> Non-standard residue type,position,sequence: w 392 2
read_al_374_> Non-standard residue type,position,sequence: w 393 2
read_al_374_> Non-standard residue type,position,sequence: w 394 2
read_al_374_> Non-standard residue type,position,sequence: w 395 2
read_al_374_> Non-standard residue type,position,sequence: w 396 2
read_al_374_> Non-standard residue type,position,sequence: w 397 2
read_al_374_> Non-standard residue type,position,sequence: w 398 2
read_al_374_> Non-standard residue type,position,sequence: w 399 2
read_al_374_> Non-standard residue type,position,sequence: w 400 2
read_al_374_> Non-standard residue type,position,sequence: w 401 2
read_al_374_> Non-standard residue type,position,sequence: w 402 2
read_al_374_> Non-standard residue type,position,sequence: w 403 2
read_al_374_> Non-standard residue type,position,sequence: w 404 2
read_al_374_> Non-standard residue type,position,sequence: w 405 2
read_al_374_> Non-standard residue type,position,sequence: w 406 2
read_al_374_> Non-standard residue type,position,sequence: w 407 2
read_al_374_> Non-standard residue type,position,sequence: w 408 2
read_al_374_> Non-standard residue type,position,sequence: w 409 2
read_al_374_> Non-standard residue type,position,sequence: w 410 2
read_al_374_> Non-standard residue type,position,sequence: w 411 2
read_al_374_> Non-standard residue type,position,sequence: w 412 2
read_al_374_> Non-standard residue type,position,sequence: w 413 2
read_al_374_> Non-standard residue type,position,sequence: w 414 2
read_al_374_> Non-standard residue type,position,sequence: w 415 2
read_al_374_> Non-standard residue type,position,sequence: w 416 2
read_al_374_> Non-standard residue type,position,sequence: w 417 2
read_al_374_> Non-standard residue type,position,sequence: w 418 2
read_al_374_> Non-standard residue type,position,sequence: w 419 2
read_al_374_> Non-standard residue type,position,sequence: w 420 2
read_al_374_> Non-standard residue type,position,sequence: w 421 2
read_al_374_> Non-standard residue type,position,sequence: w 422 2
read_al_374_> Non-standard residue type,position,sequence: w 423 2
read_al_374_> Non-standard residue type,position,sequence: w 424 2
read_al_374_> Non-standard residue type,position,sequence: w 425 2
read_al_374_> Non-standard residue type,position,sequence: w 426 2
read_al_374_> Non-standard residue type,position,sequence: w 427 2
read_al_374_> Non-standard residue type,position,sequence: w 428 2
read_al_374_> Non-standard residue type,position,sequence: w 429 2
read_al_374_> Non-standard residue type,position,sequence: w 430 2
read_al_374_> Non-standard residue type,position,sequence: w 431 2
read_al_374_> Non-standard residue type,position,sequence: w 432 2
read_al_374_> Non-standard residue type,position,sequence: w 433 2
read_al_374_> Non-standard residue type,position,sequence: w 434 2
read_al_374_> Non-standard residue type,position,sequence: w 435 2
read_al_374_> Non-standard residue type,position,sequence: w 436 2
read_al_374_> Non-standard residue type,position,sequence: w 437 2
read_al_374_> Non-standard residue type,position,sequence: w 438 2
read_al_374_> Non-standard residue type,position,sequence: w 439 2
read_al_374_> Non-standard residue type,position,sequence: w 440 2
read_al_374_> Non-standard residue type,position,sequence: w 441 2
read_al_374_> Non-standard residue type,position,sequence: w 442 2
read_al_374_> Non-standard residue type,position,sequence: w 443 2
read_al_374_> Non-standard residue type,position,sequence: w 444 2
read_al_374_> Non-standard residue type,position,sequence: w 445 2
read_al_374_> Non-standard residue type,position,sequence: w 446 2
read_al_374_> Non-standard residue type,position,sequence: w 447 2
read_al_374_> Non-standard residue type,position,sequence: w 448 2
read_al_374_> Non-standard residue type,position,sequence: w 449 2
read_al_374_> Non-standard residue type,position,sequence: w 450 2
read_al_374_> Non-standard residue type,position,sequence: w 451 2
read_al_374_> Non-standard residue type,position,sequence: w 452 2
read_al_374_> Non-standard residue type,position,sequence: w 453 2
read_al_374_> Non-standard residue type,position,sequence: w 454 2
read_al_374_> Non-standard residue type,position,sequence: w 455 2
read_al_374_> Non-standard residue type,position,sequence: w 456 2
read_al_374_> Non-standard residue type,position,sequence: w 457 2
read_al_374_> Non-standard residue type,position,sequence: w 458 2
read_al_374_> Non-standard residue type,position,sequence: w 459 2
read_al_374_> Non-standard residue type,position,sequence: w 460 2
read_al_374_> Non-standard residue type,position,sequence: w 461 2
read_al_374_> Non-standard residue type,position,sequence: w 462 2
read_al_374_> Non-standard residue type,position,sequence: w 463 2
read_al_374_> Non-standard residue type,position,sequence: w 464 2
read_al_374_> Non-standard residue type,position,sequence: w 465 2
read_al_374_> Non-standard residue type,position,sequence: w 466 2
read_al_374_> Non-standard residue type,position,sequence: w 467 2
read_al_374_> Non-standard residue type,position,sequence: w 468 2
read_al_374_> Non-standard residue type,position,sequence: w 469 2
read_al_374_> Non-standard residue type,position,sequence: w 470 2
read_al_374_> Non-standard residue type,position,sequence: w 471 2
read_al_374_> Non-standard residue type,position,sequence: w 472 2
read_al_374_> Non-standard residue type,position,sequence: w 473 2
read_al_374_> Non-standard residue type,position,sequence: w 474 2
read_al_374_> Non-standard residue type,position,sequence: w 475 2
read_al_374_> Non-standard residue type,position,sequence: w 476 2
read_al_374_> Non-standard residue type,position,sequence: w 477 2
read_al_374_> Non-standard residue type,position,sequence: w 478 2
read_al_374_> Non-standard residue type,position,sequence: w 479 2
read_al_374_> Non-standard residue type,position,sequence: w 480 2
read_al_374_> Non-standard residue type,position,sequence: w 481 2
read_al_374_> Non-standard residue type,position,sequence: w 482 2
read_al_374_> Non-standard residue type,position,sequence: w 483 2
read_al_374_> Non-standard residue type,position,sequence: w 484 2
read_al_374_> Non-standard residue type,position,sequence: w 485 2
read_al_374_> Non-standard residue type,position,sequence: w 486 2
read_al_374_> Non-standard residue type,position,sequence: w 487 2
read_al_374_> Non-standard residue type,position,sequence: w 488 2
read_al_374_> Non-standard residue type,position,sequence: w 489 2
read_al_374_> Non-standard residue type,position,sequence: w 490 2
read_al_374_> Non-standard residue type,position,sequence: w 491 2
read_al_374_> Non-standard residue type,position,sequence: w 492 2
read_al_374_> Non-standard residue type,position,sequence: w 493 2
read_al_374_> Non-standard residue type,position,sequence: w 494 2
read_al_374_> Non-standard residue type,position,sequence: w 495 2
read_al_374_> Non-standard residue type,position,sequence: w 496 2
read_al_374_> Non-standard residue type,position,sequence: w 497 2
read_al_374_> Non-standard residue type,position,sequence: w 498 2
read_al_374_> Non-standard residue type,position,sequence: w 499 2
read_al_374_> Non-standard residue type,position,sequence: w 500 2
read_al_374_> Non-standard residue type,position,sequence: w 501 2
read_al_374_> Non-standard residue type,position,sequence: w 502 2
read_al_374_> Non-standard residue type,position,sequence: w 503 2
read_al_374_> Non-standard residue type,position,sequence: w 504 2
Read the alignment from file : alignment.ali
Total number of alignment positions: 1008
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5ttu.pdb_ 775 1 5ttu.pdb_2
2 chain_A 504 1 chain_A
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5ttu.pdb_2.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1014442 990.666
0.967
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1014442 990.666
0.967
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1014613 990.833
0.968
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1015463 991.663
0.968
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1016721 992.892
0.970
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1018625 994.751
0.971
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1018625 994.751
0.971
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1018715 994.839
0.972
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1021571 997.628
0.974
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1021571 997.628
0.974
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1021706 997.760
0.974
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1025990 1001.943
0.978
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1025990 1001.943
0.978
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1026188 1002.137
0.979
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1032614 1008.412
0.985
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1032614 1008.412
0.985
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1032911 1008.702
0.985
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1042533 1018.099
0.994
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1042533 1018.099
0.994
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1042983 1018.538
0.995
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1057433 1032.649
1.008
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1057433 1032.649
1.008
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1058108 1033.309
1.009
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1079766 1054.459
1.030
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1079766 1054.459
1.030
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1080774 1055.443
1.031
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1113278 1087.186
1.062
read_pd_459W> Residue type 7KV not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type SO4 not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1113278 1087.186
1.062
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1114790 1088.662
1.063
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1117220 1091.035
1.065
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 272)
Alignment LDMLWTIFEERHLKYISQLGKGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREI
PDB LDMLW...wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
Match *****
Alignment residue type 17 (T, THR) does not match pdb
residue type 67 (., 7KV),
for align code 5ttu.pdb_2 (atom file 5ttu.pdb_2), pdb residue number " 1201",
chain "A"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 5ttu.pdb_2
No output models from Modeller; see log for Modeller text output.
> open
> /Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module1/Exercise/rcsb_pdb_5TTU.fasta
Summary of feedback from opening
/Users/kadahlst/Documents/2025/Courses/SBBM/ModuleMaterial/Module1/Exercise/rcsb_pdb_5TTU.fasta
---
notes | Alignment identifier is rcsb_pdb_5TTU.fasta
Associated 5ttu.pdb chain A to 5TTU_1|Chain A|Tyrosine-protein kinase
JAK3|Homo sapiens (9606) with 0 mismatches
Opened 1 sequence from rcsb_pdb_5TTU.fasta
> select clear
> select /A:830
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:830
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:830-834
13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected
> ui tool show "Model Loops"
> modeller refine rcsb_pdb_5TTU.fasta:1:16,20 numModels 5 fast false
> adjacentFlexible 1 protocol DOPE-HR
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 311, in launch_modeller
run(
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3248, in run
result = ci.function(
^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3900, in __call__
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3227, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/cmd.py", line 138, in model_loops
loops.model(session, targets, adjacent_flexible=adjacent_flexible,
block=block, chains=chains,
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/loops.py", line 143, in model
find_affixes(r.chain, {r.chain: (seq, None, match_map)}, aln)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/loops.py", line 307, in find_affixes
match_map = alignment.match_maps[chain]
~~~~~~~~~~~~~~~~~~~~^^^^^^^
KeyError: <chimerax.atomic.molobject.Chain object at 0x15f217050>
KeyError:
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/loops.py", line 307, in find_affixes
match_map = alignment.match_maps[chain]
~~~~~~~~~~~~~~~~~~~~^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15H0000SKS/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.121.1
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.6 (23H626)
Kernel Version: Darwin 23.6.0
Time since boot: 21 days, 7 hours, 44 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Dell S2417DG:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.4.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.9
ChimeraX-AtomicLibrary: 14.1.20
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202506232245
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.12.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.20
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.4
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.46.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (4)
comment:1 by , 4 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Modeller mismatch failure |
comment:2 by , 4 months ago
comment:3 by , 4 months ago
Hi Eric,
Thank you for the fast reply. I actually tried the earlier version where it worked before I reported, just to check if it would have been something with this specific structure or something that was messed up with what I did. This is nothing super important that I am in a hurry with :)
Good luck with the fixing!
Thanks again!
//Käthe
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, June 26, 2025 8:35:09 PM
To: Käthe Dahlström; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #18083: Modeller mismatch failure
#18083: Modeller mismatch failure
-------------------------------------------+----------------------
Reporter: kathe.dahlstrom@… | Owner: pett
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Structure Prediction | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------------+----------------------
Comment (by pett):
Hi Kathe,
Thanks for reporting this problem. I don't think it's specific to
5ttu since it also fails for other structures I tried (e.g. 1www, 6jv6).
However, it does work in the 1.10 production release, so if you use that
then you will be able to do your modeling. The Modeller interface code is
pretty complex, so it might be a few days before this gets fixed in the
daily build.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18083#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 3 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Fix will be in the next daily build.
Fix: https://github.com/RBVI/ChimeraX/commit/8424b43fc743eeb9edbb07a8cefd1eba3be105f9
Note:
See TracTickets
for help on using tickets.
Hi Kathe,
--Eric