Modeller residue indices wrong

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110211153 (2021-10-21 11:53:31 UTC)
Description
loop modeling unsuccessful, I suspect a bug since I was able to model this same missing segment in the daily build maybe a week or two ago

open 1t2p
...open its uniprot sequence
seq dissoc /a,c
... use model loops with defaults (1 flex res, missing internal segment)

Session attached

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html

executed startup.cxc  
UCSF ChimeraX version: 1.3.dev202110211153 (2021-10-21)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1t2p format mmcif fromDatabase pdb

1t2p title:  
Crystal structure of Sortase A from Staphylococcus aureus [more info...]  
  
Chain information for 1t2p #1  
---  
Chain | Description | UniProt  
A B C | sortase | Q9S446_STAAU  
  
1t2p mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
  

> open Q9S446_STAAU fromDatabase uniprot

Summary of feedback from opening Q9S446_STAAU fetched from uniprot  
---  
notes | UniProt identifier Q9S446_STAAU maps to entry Q9S446  
Alignment identifier is Q9S446_STAAU  
Associated 1t2p chain A to Q9S446_STAAU with 0 mismatches  
Associated 1t2p chain B to Q9S446_STAAU with 0 mismatches  
Associated 1t2p chain C to Q9S446_STAAU with 0 mismatches  
  
Opened UniProt Q9S446_STAAU  

> sequence dissociate /a,c

Disassociated 1t2p chain A from Q9S446_STAAU  
Disassociated 1t2p chain C from Q9S446_STAAU  

> ui tool show "Model Loops"

> modeller refine Q9S446_STAAU:1:internal-missing numModels 3 fast false
> adjacentFlexible 1 protocol standard

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service1634837130106-498868286  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1634837130106-498868286  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service1634837130106-498868286 finished  
  
Modeller error output  
Traceback (most recent call last):  
File "/usr/local/opal-local/bin/modeller9v8.py", line 332, in <module>  
main()  
File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main  
VersionMap[cf["version"]](cf)  
File "/usr/local/opal-local/bin/modeller9v8.py", line 34, in v2_run  
execfile(fn)  
File "ModellerModelling.py", line 86, in <module>  
a.make()  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py",
line 42, in make  
AutoModel.make(self, exit_stage)  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 151, in make  
atmsel = self._check_select_atoms()  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 696, in _check_select_atoms  
atmsel = self.select_atoms()  
File "ModellerModelling.py", line 38, in select_atoms  
self.residue_range(106, 85)  
File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 388,
in residue_range  
raise ValueError("End residue is before start residue")  
ValueError: End residue is before start residue  
  
  
Modeller run output  
**** IGNORE FOLLOWING LICENSE KEY MESSAGE ****  
check_lice_E> Invalid license key: xxx  
Go to https://salilab.org/modeller/ to get a license key,  
and then set the 'license' variable to it in the file  
/usr/lib/modeller10.1/modlib/modeller/config.py  
  
**** END IGNORED MESSAGE ****  
  
MODELLER 10.1, 2021/03/12, r12156  
  
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS  
  
  
Copyright(c) 1989-2021 Andrej Sali  
All Rights Reserved  
  
Written by A. Sali  
with help from  
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,  
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,  
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,  
F. Melo, J.P. Overington, E. Feyfant  
University of California, San Francisco, USA  
Rockefeller University, New York, USA  
Harvard University, Cambridge, USA  
Imperial Cancer Research Fund, London, UK  
Birkbeck College, University of London, London, UK  
  
  
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
3.10.0-1160.36.2.el7.x86_64 x86_64  
Date and time of compilation : 2021/03/12 00:18:43  
MODELLER executable type : x86_64-intel8  
Job starting time (YY/MM/DD HH:MM:SS): 2021/10/21 10:25:30  
  
environ____W> The class 'environ' is deprecated; use 'Environ' instead  
openf___224_> Open $(LIB)/restyp.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/resgrp.lib  
rdresgr_266_> Number of residue groups: 2  
openf___224_> Open ${MODINSTALL10v1}/modlib/sstruc.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183  
openf___224_> Open ${MODINSTALL10v1}/modlib/resdih.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230  
rdrdih__263_> Number of dihedral angle types : 9  
Maximal number of dihedral angle optima: 3  
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5  
openf___224_> Open ${MODINSTALL10v1}/modlib/radii.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242  
openf___224_> Open ${MODINSTALL10v1}/modlib/af_mnchdef.lib  
rdwilmo_274_> Mainchain residue conformation classes: APBLE  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch.lib  
rdclass_257_> Number of classes: 5  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch1.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch2.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch3.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/xs4.mat  
rdrrwgh_268_> Number of residue types: 21  
loopmodel__W> The class 'loopmodel' is deprecated; use 'LoopModel' 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 amaxsequence [B,KiB,MiB]: 528737 516.345 0.504  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528765 516.372 0.504  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528793 516.399 0.504  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 530501 518.067 0.506  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 531049 518.603 0.506  
  
Read the alignment from file : alignment.ali  
  
Total number of alignment positions: 428  
  
# Code #_Res #_Segm PDB_code Name  
\-------------------------------------------------------------------------------  
1 1t2p_1 428 3 1t2p_1  
2 Q9S446_ST 138 1 Q9S446_STAA  
check_a_343_> >> BEGINNING OF COMMAND  
openf___224_> Open ./1t2p_1.pdb  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 661174 645.678
0.631  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 661174 645.678 0.631  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 661345 645.845
0.631  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 662195 646.675
0.632  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 663453 647.903
0.633  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 665357 649.763
0.635  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 665357 649.763 0.635  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 665447 649.851
0.635  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 668303 652.640
0.637  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 668303 652.640 0.637  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 668438 652.771
0.637  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 672722 656.955
0.642  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 672722 656.955 0.642  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 672920 657.148
0.642  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 679346 663.424
0.648  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 679346 663.424 0.648  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 679643 663.714
0.648  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 689265 673.110
0.657  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 689265 673.110 0.657  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 689715 673.550
0.658  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 704165 687.661
0.672  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 704165 687.661 0.672  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 704165 687.661
0.672  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 704165 687.661 0.672  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 704840 688.320
0.672  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 726498 709.471
0.693  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 726498 709.471 0.693  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 727506 710.455
0.694  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 760010 742.197
0.725  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 760010 742.197 0.725  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761522 743.674
0.726  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 810278 791.287
0.773  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 809585 790.610
0.772  
  
check_ali___> Checking the sequence-structure alignment.  
  
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:  
  
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST  
\----------------------------------------------  
252 1 167 176 G D 17.215  
END OF TABLE  
check_a_344_> << END OF COMMAND  
openf___224_> Open ${LIB}/top_heav.lib  
read_to_681_> topology.submodel read from topology file: 3  
openf___224_> Open ${LIB}/par.lib  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 948837 926.599
0.905  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 950437 928.161
0.906  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 954417 932.048
0.910  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 956417 934.001
0.912  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 959417 936.931
0.915  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 963917 941.325
0.919  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 969489 946.767
0.925  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 972289 949.501
0.927  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 976489 953.603
0.931  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 982789 959.755
0.937  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 985561 962.462
0.940  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 986961 963.829
0.941  
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE  
227 561 661 112 0  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1008470 984.834 0.962  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1117740 1091.543 1.066  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1133916 1107.340 1.081  
  
mkilst______> segment topology constructed from sequence and RTF:  
segments residues atoms bonds angles dihedrals impropers:  
1 138 1096 1118 0 0 452  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1180680 1153.008 1.126  
  
patch_______> segment topology patched using RTF: 1 ; ALA ; NTER  
segments residues atoms bonds angles dihedrals impropers:  
1 138 1096 1118 1510 1792 452  
  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1234056 1205.133 1.177  
patch_______> segment topology patched using RTF: 138 ; LYS ; CTER  
segments residues atoms bonds angles dihedrals impropers:  
1 138 1097 1119 1512 1794 453  
  
genseg______> segment topology constructed from sequence and RTF:  
segments residues atoms bonds angles dihedrals impropers:  
1 138 1097 1119 1512 1794 453  
transfe_506_> MODEL is an average of all templates.  
transfe_511_> Number of templates for coordinate transfer: 1  
After transferring coordinates of the equivalent template atoms,  
there are defined, undefined atoms in MODEL: 1091 6  
openf___224_> Open Q9S446_STAAU.ini  
wrpdb___568_> Residues, atoms, selected atoms: 138 1097 1097  
make_re_417_> Restraint type to be calculated: stereo  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1341505 1310.063
1.279  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1349697 1318.063
1.287  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1366081 1334.063
1.303  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1398849 1366.063
1.334  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1431617 1398.063
1.365  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1497153 1462.063
1.428  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1529921 1494.063
1.459  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1562689 1526.063
1.490  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1628225 1590.063
1.553  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1759297 1718.063
1.678  
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.  
Added bond,angle,dihedral,improper restraints : 1119 1512 1726 444  
Total number of restraints before, now : 0 4801  
make_re_422_> Number of previous, current restraints : 0 4801  
make_re_423_> Number of previous, current selected restraints: 0 4801  
make_re_417_> Restraint type to be calculated: phi-psi_binormal  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1838272 1795.188
1.753  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch1.bin  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch1.mdt  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 147
LYS  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 148
PRO  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 284
LYS  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 147
LYS  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 148
PRO  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 284
LYS  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 147
LYS  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 148
PRO  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 284
LYS  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 147
LYS  
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 284
LYS  
getdata_643_> Protein accepted: 1t2p_1  
getdata_289_> Proteins (all/accepted): 1 1  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1903824 1859.203
1.816  
make_re_422_> Number of previous, current restraints : 4801 4937  
make_re_423_> Number of previous, current selected restraints: 4801 4937  
make_re_417_> Restraint type to be calculated: omega_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1903824 1859.203
1.816  
openf___224_> Open ${MODINSTALL10v1}/modlib/omega.bin  
openf___224_> Open ${MODINSTALL10v1}/modlib/omega.mdt  
getdata_643_> Protein accepted: 1t2p_1  
getdata_289_> Proteins (all/accepted): 1 1  
omgdel__425_> Unselected all O C +N +CA dihedrals: 146  
(This is to avoid clashes between STEREO  
and OMEGA_DIHEDRAL restraints)  
make_re_422_> Number of previous, current restraints : 4937 5074  
make_re_423_> Number of previous, current selected restraints: 4937 4928  
make_re_417_> Restraint type to be calculated: chi1_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1903824 1859.203
1.816  
openf___224_> Open ${MODINSTALL10v1}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v1}/modlib/chi1.mdt  
getdata_643_> Protein accepted: 1t2p_1  
getdata_289_> Proteins (all/accepted): 1 1  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1969360 1923.203
1.878  
make_re_422_> Number of previous, current restraints : 5074 5195  
make_re_423_> Number of previous, current selected restraints: 4928 5049  
make_re_417_> Restraint type to be calculated: chi2_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1969360 1923.203
1.878  
openf___224_> Open ${MODINSTALL10v1}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v1}/modlib/chi2.mdt  
getdata_643_> Protein accepted: 1t2p_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 5195 5289  
make_re_423_> Number of previous, current selected restraints: 5049 5143  
make_re_417_> Restraint type to be calculated: chi3_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1969360 1923.203
1.878  
openf___224_> Open ${MODINSTALL10v1}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v1}/modlib/chi3.mdt  
getdata_643_> Protein accepted: 1t2p_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 5289 5337  
make_re_423_> Number of previous, current selected restraints: 5143 5191  
make_re_417_> Restraint type to be calculated: chi4_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1969360 1923.203
1.878  
openf___224_> Open ${MODINSTALL10v1}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v1}/modlib/chi4.mdt  
mdtrsr__446W> A potential that relies on one protein is used, yet you have at  
least one known structure available. MDT, not library, potential is used.  
getdata_643_> Protein accepted: 1t2p_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 5337 5359  
make_re_423_> Number of previous, current selected restraints: 5191 5213  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2285260 2231.699
2.179  
make_re_422_> Number of previous, current restraints : 5359 7950  
make_re_423_> Number of previous, current selected restraints: 5213 7804  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2416332 2359.699
2.304  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2547404 2487.699
2.429  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2809548 2743.699
2.679  
make_re_422_> Number of previous, current restraints : 7950 10706  
make_re_423_> Number of previous, current selected restraints: 7804 10560  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2940620 2871.699
2.804  
make_re_422_> Number of previous, current restraints : 10706 13183  
make_re_423_> Number of previous, current selected restraints: 10560 13037  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 13183 14455  
make_re_423_> Number of previous, current selected restraints: 13037 14309  
0 atoms in HETATM/BLK residues constrained  
to protein atoms within 2.30 angstroms  
and protein CA atoms within 10.00 angstroms  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 14455 14455  
make_re_423_> Number of previous, current selected restraints: 14309 14309  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 14455 14455  
make_re_423_> Number of previous, current selected restraints: 14309 14309  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 14455 14455  
make_re_423_> Number of previous, current selected restraints: 14309 14309  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 14455 14455  
make_re_423_> Number of previous, current selected restraints: 14309 14309  
0 atoms in residues without defined topology  
constrained to be rigid bodies  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 14455 14455  
make_re_423_> Number of previous, current selected restraints: 14309 14309  
rmdupl__427_> 874 redundant cosine dihedral restraints were unselected.  
condens_443_> Restraints marked for deletion were removed.  
Total number of restraints before, now: 14455 13435  
openf___224_> Open Q9S446_STAAU.rsr  
openf___224_> Open Q9S446_STAAU.rsr  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2576956 2516.559
2.458  
rdcsr2__307_> Number of restraints read : 13435  
Number of excluded pairs read: 0  
Number of pseudo atoms read : 0  
rdcsrs__304_> Restraints in memory, selected restraints: 13435 13435  
Explicitly excluded atom pairs in memory : 0  
Pseudo atoms in memory : 0  
  
No output models from Modeller; see log for Modeller text output.  

> save bloop.cxs




OpenGL version: 4.1 INTEL-14.7.18
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 427.140.8.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1419)
      Kernel Version: Darwin 19.6.0
      Time since boot: 2:11

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110211153
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.3
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.2
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.6
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
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    sfftk-rw: 0.7.1
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    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
File attachment: bloop.cxs

bloop.cxs​

[Elaine Meng]

Added by email2trac

[Eric Pettersen]

FYI, it works when using the non-UniProt sequence.

[Eric Pettersen]

For the UniProt sequence it remodels well past the point it should, whereas for the chain sequence the remodeling stops at the expected point.

[Eric Pettersen]

Okay, even *more* fixed now! :-)