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Opened 17 months ago
Closed 17 months ago
#15263 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-348.el8.0.2.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000147d9686d740 (most recent call first):
Garbage-collecting
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/selectors.py", line 356 in _update_select_residues_menu
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/selectors.py", line 242 in
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.mmcif.mmcif_write (total: 53)
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-21.cif
Summary of feedback from opening
/yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-21.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 19
Unable to fetch template for '---': will connect using distance criteria
Unknown polymer entity '2' near line 229
Unknown polymer entity '84' near line 336
Unknown polymer entity '3' near line 345
Unknown polymer entity '85' near line 6724
Unknown polymer entity '4' near line 6752
99 messages similar to the above omitted
Skipping residue with duplicate label_seq_id -32767 in chain
Skipping residue with duplicate label_seq_id -32767 in chain
Skipping residue with duplicate label_seq_id -32767 in chain
Atom . is not in the residue template for LEU /CA:302
Atom . is not in the residue template for PRO /Lq:201
Atom . is not in the residue template for GLU /Lq:202
Atom . is not in the residue template for VAL /Lq:203
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for
Class10_FR_EF2_merged_may20_real_space_refined_008-coot-21.cif #1
---
Chain | Description
CA | No description available
CB | No description available
CC | No description available
CD | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lq | No description available
Lr | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> save
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-21_chimerax.pdb
> relModel #1
Chain IDs longer than 2 characters; truncating
> close
> set bgColor white
> set bgColor #ffffff00
> open
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-0.pdb
Chain information for
Class10_FR_EF2_merged_may20_real_space_refined_008-coot-0.pdb #1
---
Chain | Description
2 | No description available
5 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
> ui mousemode right select
Drag select of 1 atoms
> delete atoms sel
> delete bonds sel
> save
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-0.cif
> relModel #1
Not saving entity_poly_seq for non-authoritative sequences
QXcbConnection: XCB error: 3 (BadWindow), sequence: 42753, resource id:
9387103, major code: 40 (TranslateCoords), minor code: 0
> save
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-0.pdb
> relModel #1
QXcbConnection: XCB error: 3 (BadWindow), sequence: 46505, resource id:
9404312, major code: 40 (TranslateCoords), minor code: 0
> close
> open
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-0.cif
Summary of feedback from opening
/yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-0.cif
---
warnings | Unable to fetch template for 'US': will connect using distance
criteria
Unknown polymer entity '1' near line 429
Unable to fetch template for 'A2MS': will connect using distance criteria
Unable to fetch template for 'PSUS': will connect using distance criteria
Unable to fetch template for 'OMUS': will connect using distance criteria
Unable to fetch template for 'OMCS': will connect using distance criteria
Unable to fetch template for 'OMGS': will connect using distance criteria
75 messages similar to the above omitted
Invalid residue range for struct_conf "HELX1": invalid entity "5", near line
466887
Invalid residue range for struct_conf "HELX2": invalid entity "6", near line
466888
Invalid residue range for struct_conf "HELX3": invalid entity "6", near line
466889
Invalid residue range for struct_conf "HELX4": invalid entity "6", near line
466890
Invalid residue range for struct_conf "HELX5": invalid entity "6", near line
466891
468 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid entity "6", near
line 467852
Invalid sheet range for struct_sheet_range "? 2": invalid entity "6", near
line 467853
Invalid sheet range for struct_sheet_range "? 3": invalid entity "6", near
line 467854
Invalid sheet range for struct_sheet_range "? 4": invalid entity "6", near
line 467855
Invalid sheet range for struct_sheet_range "? 5": invalid entity "6", near
line 467856
399 messages similar to the above omitted
Atom OP2 is not in the residue template for AS /2:2
Atom P is not in the residue template for CS /2:3
Atom P is not in the residue template for CS /2:4
Atom OP2 is not in the residue template for GS /2:6
Atom OP2 is not in the residue template for GS /2:7
Atom OP2 is not in the residue template for GS /2:10
Atom OP2 is not in the residue template for AS /2:11
Atom P is not in the residue template for CS /2:13
Atom P is not in the residue template for CS /2:14
Atom OP2 is not in the residue template for GS /2:16
Atom P is not in the residue template for CS /2:17
Atom P is not in the residue template for CS /2:18
Atom OP2 is not in the residue template for AS /2:19
Atom OP2 is not in the residue template for GS /2:20
Atom OP2 is not in the residue template for AS /2:22
Atom OP2 is not in the residue template for GS /2:23
Atom P is not in the residue template for CS /2:24
Atom OP2 is not in the residue template for AS /2:25
Atom OP2 is not in the residue template for GS /2:29
Atom P is not in the residue template for CS /2:30
Atom OP2 is not in the residue template for GS /2:33
Atom P is not in the residue template for CS /2:35
Atom P is not in the residue template for CS /2:37
Atom OP2 is not in the residue template for AS /2:38
Atom OP2 is not in the residue template for AS /2:39
Atom OP2 is not in the residue template for AS /2:40
Atom OP2 is not in the residue template for GS /2:41
Atom OP2 is not in the residue template for AS /2:42
3 messages similar to the above omitted
Atom P is not in the residue template for CS /2:48
Atom P is not in the residue template for CS /2:49
Atom OP2 is not in the residue template for AS /2:50
Atom OP2 is not in the residue template for GS /2:52
Atom P is not in the residue template for CS /2:53
Atom OP2 is not in the residue template for AS /2:54
Atom OP2 is not in the residue template for GS /2:56
Atom P is not in the residue template for CS /2:58
Atom OP2 is not in the residue template for AS /2:60
Atom OP2 is not in the residue template for AS /2:61
Atom OP2 is not in the residue template for GS /2:62
Atom OP2 is not in the residue template for AS /2:64
Atom P is not in the residue template for CS /2:65
Atom OP2 is not in the residue template for GS /2:66
Atom P is not in the residue template for CS /2:67
Atom OP2 is not in the residue template for AS /2:68
Atom P is not in the residue template for CS /2:69
Atom OP2 is not in the residue template for GS /2:70
Atom OP2 is not in the residue template for GS /2:71
Atom P is not in the residue template for CS /2:72
Atom OP2 is not in the residue template for AS /2:77
Atom P is not in the residue template for CS /2:78
Atom OP2 is not in the residue template for AS /2:79
Atom OP2 is not in the residue template for GS /2:80
Atom OP2 is not in the residue template for GS /2:82
Atom OP2 is not in the residue template for AS /2:83
Atom OP2 is not in the residue template for AS /2:84
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:86
Atom OP2 is not in the residue template for GS /2:88
Atom P is not in the residue template for CS /2:89
Atom OP2 is not in the residue template for GS /2:90
Atom OP2 is not in the residue template for AS /2:91
Atom OP2 is not in the residue template for AS /2:92
Atom OP2 is not in the residue template for GS /2:94
Atom OP2 is not in the residue template for GS /2:95
Atom P is not in the residue template for CS /2:96
Atom P is not in the residue template for CS /2:98
Atom OP2 is not in the residue template for AS /2:102
Atom OP2 is not in the residue template for AS /2:103
Atom OP2 is not in the residue template for AS /2:104
Atom P is not in the residue template for CS /2:106
Atom OP2 is not in the residue template for AS /2:107
Atom OP2 is not in the residue template for GS /2:108
Atom OP2 is not in the residue template for AS /2:111
Atom OP2 is not in the residue template for GS /2:113
Atom OP2 is not in the residue template for GS /2:114
Atom P is not in the residue template for CS /2:117
Atom P is not in the residue template for CS /2:118
Atom OP2 is not in the residue template for GS /2:122
Atom OP2 is not in the residue template for GS /2:123
Atom P is not in the residue template for CS /2:125
Atom OP2 is not in the residue template for GS /2:126
Atom P is not in the residue template for CS /2:127
Atom P is not in the residue template for CS /2:129
Atom OP2 is not in the residue template for GS /2:130
Atom P is not in the residue template for CS /2:140
Atom OP2 is not in the residue template for AS /2:141
Atom P is not in the residue template for CS /2:142
Atom OP2 is not in the residue template for GS /2:145
Atom OP2 is not in the residue template for GS /2:146
Atom OP2 is not in the residue template for AS /2:147
Atom OP2 is not in the residue template for AS /2:149
Atom OP2 is not in the residue template for AS /2:150
Atom P is not in the residue template for CS /2:151
Atom OP2 is not in the residue template for GS /2:153
Atom OP2 is not in the residue template for GS /2:155
Atom OP2 is not in the residue template for GS /2:156
Atom OP2 is not in the residue template for AS /2:158
Atom P is not in the residue template for CS /2:162
Atom OP2 is not in the residue template for AS /2:164
Atom OP2 is not in the residue template for GS /2:165
Atom OP2 is not in the residue template for GS /2:167
Atom P is not in the residue template for CS /2:168
Atom OP2 is not in the residue template for AS /2:170
Atom OP2 is not in the residue template for AS /2:171
Atom OP2 is not in the residue template for AS /2:173
Atom OP2 is not in the residue template for AS /2:175
Atom OP2 is not in the residue template for GS /2:177
Atom P is not in the residue template for CS /2:178
Atom P is not in the residue template for CS /2:179
Atom OP2 is not in the residue template for GS /2:180
Atom OP2 is not in the residue template for AS /2:181
Atom P is not in the residue template for CS /2:182
Atom OP2 is not in the residue template for GS /2:183
Atom OP2 is not in the residue template for GS /2:184
Atom OP2 is not in the residue template for GS /2:185
Atom P is not in the residue template for CS /2:186
Atom OP2 is not in the residue template for GS /2:187
Atom P is not in the residue template for CS /2:188
Atom OP2 is not in the residue template for GS /2:190
Atom OP2 is not in the residue template for AS /2:191
Atom P is not in the residue template for CS /2:192
Atom P is not in the residue template for CS /2:193
Atom P is not in the residue template for CS /2:194
Atom OP2 is not in the residue template for GS /2:203
Atom OP2 is not in the residue template for GS /2:204
Atom OP2 is not in the residue template for GS /2:205
Atom OP2 is not in the residue template for GS /2:206
Atom OP2 is not in the residue template for GS /2:207
3 messages similar to the above omitted
Atom P is not in the residue template for CS /2:212
Atom OP2 is not in the residue template for GS /2:213
Atom OP2 is not in the residue template for GS /2:215
Atom P is not in the residue template for CS /2:216
Atom OP2 is not in the residue template for AS /2:217
Atom OP2 is not in the residue template for AS /2:221
Atom P is not in the residue template for CS /2:223
Atom OP2 is not in the residue template for AS /2:224
Atom OP2 is not in the residue template for GS /2:225
Atom OP2 is not in the residue template for GS /2:288
Atom OP2 is not in the residue template for GS /2:289
Atom OP2 is not in the residue template for GS /2:291
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:293
Atom P is not in the residue template for CS /2:295
Atom OP2 is not in the residue template for AS /2:297
Atom OP2 is not in the residue template for GS /2:298
Atom OP2 is not in the residue template for AS /2:299
Atom OP2 is not in the residue template for AS /2:301
Atom OP2 is not in the residue template for AS /2:302
Atom P is not in the residue template for CS /2:303
Atom P is not in the residue template for CS /2:304
Atom P is not in the residue template for CS /2:306
Atom OP2 is not in the residue template for GS /2:307
Atom OP2 is not in the residue template for GS /2:308
Atom OP2 is not in the residue template for GS /2:309
Atom P is not in the residue template for CS /2:310
Atom P is not in the residue template for CS /2:311
Atom OP2 is not in the residue template for GS /2:312
Atom OP2 is not in the residue template for AS /2:313
Atom P is not in the residue template for CS /2:315
Atom OP2 is not in the residue template for GS /2:316
Atom P is not in the residue template for CS /2:317
Atom OP2 is not in the residue template for AS /2:318
Atom P is not in the residue template for CS /2:319
Atom OP2 is not in the residue template for GS /2:320
Atom P is not in the residue template for CS /2:321
Atom P is not in the residue template for CS /2:322
Atom P is not in the residue template for CS /2:323
Atom OP2 is not in the residue template for GS /2:327
Atom OP2 is not in the residue template for GS /2:329
Atom OP2 is not in the residue template for GS /2:330
Atom P is not in the residue template for CS /2:331
Atom OP2 is not in the residue template for GS /2:332
Atom OP2 is not in the residue template for GS /2:333
Atom P is not in the residue template for CS /2:334
Atom OP2 is not in the residue template for GS /2:335
Atom OP2 is not in the residue template for AS /2:336
Atom P is not in the residue template for CS /2:337
Atom OP2 is not in the residue template for GS /2:338
Atom OP2 is not in the residue template for AS /2:339
Atom P is not in the residue template for CS /2:340
Atom P is not in the residue template for CS /2:341
Atom P is not in the residue template for CS /2:342
Atom OP2 is not in the residue template for AS /2:343
Atom P is not in the residue template for CS /2:346
Atom OP2 is not in the residue template for GS /2:347
Atom OP2 is not in the residue template for AS /2:348
Atom OP2 is not in the residue template for AS /2:349
Atom P is not in the residue template for CS /2:350
Atom OP2 is not in the residue template for GS /2:351
Atom P is not in the residue template for CS /2:353
Atom OP2 is not in the residue template for GS /2:355
Atom P is not in the residue template for CS /2:356
Atom P is not in the residue template for CS /2:357
Atom P is not in the residue template for CS /2:358
Atom OP2 is not in the residue template for AS /2:360
Atom P is not in the residue template for CS /2:362
Atom OP2 is not in the residue template for AS /2:363
Atom OP2 is not in the residue template for AS /2:364
Atom P is not in the residue template for CS /2:365
Atom P is not in the residue template for CS /2:369
Atom OP2 is not in the residue template for GS /2:370
Atom OP2 is not in the residue template for AS /2:371
Atom OP2 is not in the residue template for GS /2:373
Atom OP2 is not in the residue template for GS /2:374
Atom OP2 is not in the residue template for AS /2:376
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:379
Atom OP2 is not in the residue template for GS /2:380
Atom P is not in the residue template for CS /2:381
Atom P is not in the residue template for CS /2:382
Atom OP2 is not in the residue template for GS /2:383
Atom OP2 is not in the residue template for GS /2:385
Atom P is not in the residue template for CS /2:386
Atom P is not in the residue template for CS /2:387
Atom OP2 is not in the residue template for AS /2:389
Atom P is not in the residue template for CS /2:390
Atom P is not in the residue template for CS /2:391
Atom OP2 is not in the residue template for AS /2:392
Atom OP2 is not in the residue template for GS /2:394
Atom OP2 is not in the residue template for GS /2:395
Atom OP2 is not in the residue template for GS /2:397
Atom OP2 is not in the residue template for AS /2:398
Atom P is not in the residue template for CS /2:399
Atom P is not in the residue template for CS /2:400
Atom OP2 is not in the residue template for AS /2:401
Atom P is not in the residue template for CS /2:402
Atom OP2 is not in the residue template for GS /2:403
Atom OP2 is not in the residue template for GS /2:404
Atom OP2 is not in the residue template for GS /2:405
Atom OP2 is not in the residue template for GS /2:407
Atom OP2 is not in the residue template for AS /2:408
Atom P is not in the residue template for CS /2:409
Atom OP2 is not in the residue template for GS /2:410
Atom OP2 is not in the residue template for GS /2:411
Atom OP2 is not in the residue template for GS /2:412
Atom OP2 is not in the residue template for GS /2:413
Atom OP2 is not in the residue template for AS /2:414
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:417
Atom OP2 is not in the residue template for AS /2:418
Atom OP2 is not in the residue template for GS /2:419
Atom OP2 is not in the residue template for GS /2:420
Atom OP2 is not in the residue template for GS /2:421
Atom P is not in the residue template for CS /2:424
Atom OP2 is not in the residue template for GS /2:425
Atom OP2 is not in the residue template for AS /2:426
Atom P is not in the residue template for CS /2:429
Atom P is not in the residue template for CS /2:430
Atom OP2 is not in the residue template for GS /2:431
Atom OP2 is not in the residue template for GS /2:432
Atom OP2 is not in the residue template for AS /2:433
Atom OP2 is not in the residue template for GS /2:434
Atom OP2 is not in the residue template for AS /2:435
4 messages similar to the above omitted
Atom P is not in the residue template for CS /2:441
Atom P is not in the residue template for CS /2:442
Atom OP2 is not in the residue template for GS /2:444
Atom OP2 is not in the residue template for AS /2:445
Atom OP2 is not in the residue template for GS /2:446
Atom OP2 is not in the residue template for AS /2:447
Atom OP2 is not in the residue template for AS /2:448
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:450
Atom OP2 is not in the residue template for GS /2:451
Atom OP2 is not in the residue template for GS /2:452
Atom P is not in the residue template for CS /2:453
Atom OP2 is not in the residue template for AS /2:455
Atom P is not in the residue template for CS /2:456
Atom P is not in the residue template for CS /2:457
Atom OP2 is not in the residue template for AS /2:458
Atom P is not in the residue template for CS /2:459
Atom OP2 is not in the residue template for AS /2:460
Atom P is not in the residue template for CS /2:462
Atom P is not in the residue template for CS /2:463
Atom OP2 is not in the residue template for AS /2:464
Atom OP2 is not in the residue template for AS /2:465
Atom OP2 is not in the residue template for GS /2:466
Atom OP2 is not in the residue template for GS /2:467
Atom OP2 is not in the residue template for AS /2:469
2 messages similar to the above omitted
Atom P is not in the residue template for CS /2:472
Atom OP2 is not in the residue template for AS /2:473
Atom OP2 is not in the residue template for GS /2:474
Atom P is not in the residue template for CS /2:475
Atom OP2 is not in the residue template for AS /2:476
Atom OP2 is not in the residue template for GS /2:477
Atom OP2 is not in the residue template for GS /2:478
Atom P is not in the residue template for CS /2:479
Atom OP2 is not in the residue template for GS /2:480
Atom P is not in the residue template for CS /2:481
Atom OP2 is not in the residue template for GS /2:482
Atom P is not in the residue template for CS /2:483
Atom OP2 is not in the residue template for AS /2:485
Atom OP2 is not in the residue template for AS /2:486
Atom OP2 is not in the residue template for AS /2:489
Atom P is not in the residue template for CS /2:490
Atom P is not in the residue template for CS /2:491
Atom P is not in the residue template for CS /2:492
Atom OP2 is not in the residue template for AS /2:493
Atom P is not in the residue template for CS /2:494
Atom P is not in the residue template for CS /2:496
Atom P is not in the residue template for CS /2:497
Atom P is not in the residue template for CS /2:498
Atom OP2 is not in the residue template for GS /2:499
Atom OP2 is not in the residue template for AS /2:500
Atom P is not in the residue template for CS /2:501
Atom P is not in the residue template for CS /2:502
Atom P is not in the residue template for CS /2:503
Atom OP2 is not in the residue template for GS /2:504
Atom OP2 is not in the residue template for GS /2:505
Atom OP2 is not in the residue template for GS /2:506
Atom OP2 is not in the residue template for GS /2:507
Atom OP2 is not in the residue template for AS /2:508
12 messages similar to the above omitted
Atom P is not in the residue template for CS /2:527
Atom OP2 is not in the residue template for AS /2:528
Atom OP2 is not in the residue template for AS /2:529
Atom OP2 is not in the residue template for AS /2:531
Atom P is not in the residue template for CS /2:532
Atom OP2 is not in the residue template for AS /2:533
Atom OP2 is not in the residue template for GS /2:534
Atom OP2 is not in the residue template for GS /2:535
Atom P is not in the residue template for CS /2:550
Atom OP2 is not in the residue template for GS /2:552
Atom OP2 is not in the residue template for AS /2:554
Atom OP2 is not in the residue template for AS /2:555
Atom OP2 is not in the residue template for GS /2:558
Atom OP2 is not in the residue template for GS /2:559
5 messages similar to the above omitted
Atom P is not in the residue template for CS /2:567
Atom P is not in the residue template for CS /2:568
Atom OP2 is not in the residue template for AS /2:569
Atom P is not in the residue template for CS /2:570
Atom OP2 is not in the residue template for AS /2:574
Atom OP2 is not in the residue template for AS /2:575
Atom P is not in the residue template for CS /2:578
Atom P is not in the residue template for CS /2:579
Atom OP2 is not in the residue template for AS /2:583
Atom OP2 is not in the residue template for AS /2:584
Atom P is not in the residue template for CS /2:585
Atom OP2 is not in the residue template for GS /2:586
Atom OP2 is not in the residue template for AS /2:587
Atom OP2 is not in the residue template for GS /2:588
Atom OP2 is not in the residue template for GS /2:589
Atom P is not in the residue template for CS /2:592
Atom P is not in the residue template for CS /2:593
Atom OP2 is not in the residue template for AS /2:594
Atom OP2 is not in the residue template for GS /2:597
Atom OP2 is not in the residue template for GS /2:598
Atom OP2 is not in the residue template for AS /2:599
Atom OP2 is not in the residue template for GS /2:600
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:603
Atom OP2 is not in the residue template for AS /2:604
Atom OP2 is not in the residue template for AS /2:605
Atom OP2 is not in the residue template for GS /2:606
Atom P is not in the residue template for CS /2:608
Atom OP2 is not in the residue template for GS /2:610
Atom OP2 is not in the residue template for GS /2:611
Atom OP2 is not in the residue template for GS /2:613
Atom P is not in the residue template for CS /2:614
Atom P is not in the residue template for CS /2:615
Atom OP2 is not in the residue template for AS /2:616
Atom OP2 is not in the residue template for GS /2:617
Atom P is not in the residue template for CS /2:618
Atom OP2 is not in the residue template for AS /2:619
Atom OP2 is not in the residue template for GS /2:620
Atom P is not in the residue template for CS /2:621
Atom P is not in the residue template for CS /2:622
Atom OP2 is not in the residue template for GS /2:623
Atom P is not in the residue template for CS /2:624
Atom OP2 is not in the residue template for GS /2:625
Atom OP2 is not in the residue template for GS /2:626
Atom OP2 is not in the residue template for AS /2:628
Atom OP2 is not in the residue template for AS /2:629
Atom P is not in the residue template for CS /2:632
Atom P is not in the residue template for CS /2:633
Atom OP2 is not in the residue template for AS /2:634
Atom OP2 is not in the residue template for GS /2:635
Atom P is not in the residue template for CS /2:636
Atom P is not in the residue template for CS /2:638
Atom P is not in the residue template for CS /2:639
Atom OP2 is not in the residue template for AS /2:640
Atom OP2 is not in the residue template for AS /2:641
Atom OP2 is not in the residue template for AS /2:643
Atom P is not in the residue template for CS /2:645
Atom OP2 is not in the residue template for GS /2:646
Atom OP2 is not in the residue template for AS /2:648
Atom OP2 is not in the residue template for AS /2:650
Atom OP2 is not in the residue template for AS /2:653
Atom OP2 is not in the residue template for AS /2:654
3 messages similar to the above omitted
Atom P is not in the residue template for CS /2:660
Atom OP2 is not in the residue template for GS /2:662
Atom P is not in the residue template for CS /2:663
Atom OP2 is not in the residue template for AS /2:664
Atom OP2 is not in the residue template for GS /2:665
Atom OP2 is not in the residue template for AS /2:668
Atom OP2 is not in the residue template for AS /2:669
Atom OP2 is not in the residue template for AS /2:670
3 messages similar to the above omitted
Atom P is not in the residue template for CS /2:674
Atom P is not in the residue template for CS /2:676
Atom OP2 is not in the residue template for GS /2:677
Atom OP2 is not in the residue template for AS /2:679
Atom OP2 is not in the residue template for GS /2:680
Atom OP2 is not in the residue template for GS /2:684
Atom OP2 is not in the residue template for AS /2:685
Atom P is not in the residue template for CS /2:687
Atom OP2 is not in the residue template for GS /2:690
Atom OP2 is not in the residue template for GS /2:691
Atom P is not in the residue template for CS /2:746
Atom P is not in the residue template for CS /2:748
Atom OP2 is not in the residue template for AS /2:802
Atom P is not in the residue template for CS /2:803
Atom OP2 is not in the residue template for GS /2:807
Atom OP2 is not in the residue template for AS /2:808
Atom OP2 is not in the residue template for AS /2:809
Atom OP2 is not in the residue template for AS /2:810
Atom OP2 is not in the residue template for AS /2:811
7 messages similar to the above omitted
Atom P is not in the residue template for CS /2:824
Atom OP2 is not in the residue template for AS /2:825
Atom OP2 is not in the residue template for AS /2:826
Atom OP2 is not in the residue template for AS /2:827
Atom OP2 is not in the residue template for GS /2:828
Atom P is not in the residue template for CS /2:829
Atom OP2 is not in the residue template for AS /2:830
Atom OP2 is not in the residue template for GS /2:831
Atom OP2 is not in the residue template for GS /2:832
Atom P is not in the residue template for CS /2:833
Atom P is not in the residue template for CS /2:834
Atom OP2 is not in the residue template for GS /2:841
Atom P is not in the residue template for CS /2:842
Atom P is not in the residue template for CS /2:843
Atom OP2 is not in the residue template for GS /2:845
Atom OP2 is not in the residue template for GS /2:846
Atom OP2 is not in the residue template for AS /2:847
Atom OP2 is not in the residue template for AS /2:849
Atom P is not in the residue template for CS /2:850
Atom P is not in the residue template for CS /2:851
Atom OP2 is not in the residue template for GS /2:852
Atom P is not in the residue template for CS /2:853
Atom OP2 is not in the residue template for AS /2:854
Atom OP2 is not in the residue template for GS /2:855
Atom P is not in the residue template for CS /2:856
Atom OP2 is not in the residue template for AS /2:858
Atom OP2 is not in the residue template for GS /2:859
Atom OP2 is not in the residue template for GS /2:860
Atom OP2 is not in the residue template for AS /2:861
Atom OP2 is not in the residue template for AS /2:862
10 messages similar to the above omitted
Atom P is not in the residue template for CS /2:876
Atom P is not in the residue template for CS /2:877
Atom OP2 is not in the residue template for GS /2:878
Atom P is not in the residue template for CS /2:879
Atom OP2 is not in the residue template for GS /2:880
Atom OP2 is not in the residue template for GS /2:881
Atom P is not in the residue template for CS /2:884
Atom P is not in the residue template for CS /2:905
Atom OP2 is not in the residue template for GS /2:907
Atom OP2 is not in the residue template for AS /2:908
Atom OP2 is not in the residue template for GS /2:909
Atom OP2 is not in the residue template for GS /2:910
Atom P is not in the residue template for CS /2:911
Atom P is not in the residue template for CS /2:912
Atom OP2 is not in the residue template for AS /2:913
Atom OP2 is not in the residue template for GS /2:915
Atom OP2 is not in the residue template for AS /2:916
Atom OP2 is not in the residue template for AS /2:919
Atom OP2 is not in the residue template for AS /2:920
6 messages similar to the above omitted
Atom P is not in the residue template for CS /2:927
Atom OP2 is not in the residue template for GS /2:928
Atom OP2 is not in the residue template for GS /2:929
Atom P is not in the residue template for CS /2:930
Atom P is not in the residue template for CS /2:931
Atom OP2 is not in the residue template for GS /2:932
Atom OP2 is not in the residue template for GS /2:933
Atom OP2 is not in the residue template for GS /2:934
Atom OP2 is not in the residue template for GS /2:935
Atom OP2 is not in the residue template for GS /2:936
Atom P is not in the residue template for CS /2:937
Atom OP2 is not in the residue template for AS /2:938
Atom P is not in the residue template for CS /2:941
Atom OP2 is not in the residue template for GS /2:942
Atom OP2 is not in the residue template for AS /2:944
Atom OP2 is not in the residue template for GS /2:947
Atom P is not in the residue template for CS /2:948
Atom OP2 is not in the residue template for GS /2:949
Atom P is not in the residue template for CS /2:950
Atom P is not in the residue template for CS /2:951
Atom OP2 is not in the residue template for GS /2:952
Atom P is not in the residue template for CS /2:953
Atom OP2 is not in the residue template for AS /2:955
Atom OP2 is not in the residue template for GS /2:956
Atom OP2 is not in the residue template for AS /2:957
Atom OP2 is not in the residue template for GS /2:958
Atom OP2 is not in the residue template for GS /2:959
4 messages similar to the above omitted
Atom P is not in the residue template for CS /2:967
Atom OP2 is not in the residue template for GS /2:970
Atom OP2 is not in the residue template for GS /2:971
Atom OP2 is not in the residue template for AS /2:972
Atom P is not in the residue template for CS /2:973
Atom P is not in the residue template for CS /2:974
Atom OP2 is not in the residue template for GS /2:975
Atom OP2 is not in the residue template for GS /2:976
Atom P is not in the residue template for CS /2:977
Atom OP2 is not in the residue template for GS /2:978
Atom P is not in the residue template for CS /2:979
Atom OP2 is not in the residue template for AS /2:980
Atom OP2 is not in the residue template for AS /2:981
Atom OP2 is not in the residue template for GS /2:982
Atom OP2 is not in the residue template for AS /2:983
Atom P is not in the residue template for CS /2:984
Atom OP2 is not in the residue template for GS /2:985
Atom OP2 is not in the residue template for GS /2:986
Atom OP2 is not in the residue template for AS /2:987
Atom P is not in the residue template for CS /2:988
Atom P is not in the residue template for CS /2:989
Atom OP2 is not in the residue template for AS /2:990
Atom OP2 is not in the residue template for GS /2:991
Atom OP2 is not in the residue template for AS /2:992
Atom OP2 is not in the residue template for GS /2:993
Atom P is not in the residue template for CS /2:994
Atom OP2 is not in the residue template for GS /2:995
Atom OP2 is not in the residue template for AS /2:996
Atom OP2 is not in the residue template for AS /2:997
Atom OP2 is not in the residue template for AS /2:998
Atom OP2 is not in the residue template for GS /2:999
Atom P is not in the residue template for CS /2:1000
Atom OP2 is not in the residue template for AS /2:1001
Atom OP2 is not in the residue template for GS /2:1005
Atom P is not in the residue template for CS /2:1006
Atom P is not in the residue template for CS /2:1007
Atom OP2 is not in the residue template for AS /2:1008
Atom OP2 is not in the residue template for AS /2:1009
Atom OP2 is not in the residue template for GS /2:1010
Atom OP2 is not in the residue template for AS /2:1011
Atom OP2 is not in the residue template for AS /2:1012
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1019
Atom OP2 is not in the residue template for AS /2:1020
Atom OP2 is not in the residue template for AS /2:1023
Atom OP2 is not in the residue template for AS /2:1024
Atom P is not in the residue template for CS /2:1026
Atom OP2 is not in the residue template for AS /2:1027
Atom OP2 is not in the residue template for AS /2:1028
Atom OP2 is not in the residue template for GS /2:1029
Atom OP2 is not in the residue template for AS /2:1030
Atom P is not in the residue template for CS /2:1032
Atom OP2 is not in the residue template for GS /2:1033
Atom OP2 is not in the residue template for AS /2:1034
Atom OP2 is not in the residue template for AS /2:1035
Atom OP2 is not in the residue template for AS /2:1036
Atom OP2 is not in the residue template for GS /2:1037
Atom P is not in the residue template for CS /2:1039
Atom OP2 is not in the residue template for GS /2:1040
Atom OP2 is not in the residue template for GS /2:1041
Atom OP2 is not in the residue template for AS /2:1042
Atom OP2 is not in the residue template for GS /2:1043
Atom OP2 is not in the residue template for GS /2:1044
Atom P is not in the residue template for CS /2:1047
Atom OP2 is not in the residue template for GS /2:1048
Atom OP2 is not in the residue template for AS /2:1049
Atom OP2 is not in the residue template for AS /2:1050
Atom OP2 is not in the residue template for GS /2:1051
Atom OP2 is not in the residue template for AS /2:1052
Atom P is not in the residue template for CS /2:1053
Atom OP2 is not in the residue template for GS /2:1054
Atom OP2 is not in the residue template for AS /2:1055
Atom P is not in the residue template for CS /2:1057
Atom OP2 is not in the residue template for AS /2:1058
Atom OP2 is not in the residue template for GS /2:1059
Atom OP2 is not in the residue template for AS /2:1060
Atom OP2 is not in the residue template for AS /2:1062
Atom P is not in the residue template for CS /2:1063
Atom P is not in the residue template for CS /2:1064
Atom OP2 is not in the residue template for GS /2:1065
Atom P is not in the residue template for CS /2:1067
Atom OP2 is not in the residue template for GS /2:1068
Atom OP2 is not in the residue template for AS /2:1070
Atom OP2 is not in the residue template for GS /2:1071
Atom P is not in the residue template for CS /2:1074
Atom P is not in the residue template for CS /2:1075
Atom OP2 is not in the residue template for GS /2:1076
Atom OP2 is not in the residue template for AS /2:1077
Atom P is not in the residue template for CS /2:1078
Atom P is not in the residue template for CS /2:1079
Atom OP2 is not in the residue template for AS /2:1080
Atom OP2 is not in the residue template for AS /2:1082
Atom OP2 is not in the residue template for AS /2:1083
Atom OP2 is not in the residue template for AS /2:1084
Atom P is not in the residue template for CS /2:1085
Atom OP2 is not in the residue template for GS /2:1086
Atom OP2 is not in the residue template for AS /2:1087
Atom OP2 is not in the residue template for GS /2:1089
Atom P is not in the residue template for CS /2:1090
Atom P is not in the residue template for CS /2:1091
Atom OP2 is not in the residue template for GS /2:1092
Atom OP2 is not in the residue template for AS /2:1093
Atom P is not in the residue template for CS /2:1094
Atom P is not in the residue template for CS /2:1095
Atom OP2 is not in the residue template for GS /2:1096
Atom OP2 is not in the residue template for GS /2:1097
Atom P is not in the residue template for CS /2:1098
Atom OP2 is not in the residue template for GS /2:1099
Atom OP2 is not in the residue template for AS /2:1100
Atom OP2 is not in the residue template for GS /2:1102
Atom P is not in the residue template for CS /2:1103
Atom OP2 is not in the residue template for GS /2:1104
Atom OP2 is not in the residue template for GS /2:1105
Atom P is not in the residue template for CS /2:1106
Atom OP2 is not in the residue template for GS /2:1107
Atom OP2 is not in the residue template for GS /2:1108
Atom P is not in the residue template for CS /2:1109
Atom OP2 is not in the residue template for GS /2:1110
Atom OP2 is not in the residue template for AS /2:1113
Atom P is not in the residue template for CS /2:1116
Atom P is not in the residue template for CS /2:1117
Atom P is not in the residue template for CS /2:1118
Atom OP2 is not in the residue template for AS /2:1119
Atom OP2 is not in the residue template for GS /2:1121
Atom OP2 is not in the residue template for AS /2:1122
Atom P is not in the residue template for CS /2:1123
Atom P is not in the residue template for CS /2:1124
Atom P is not in the residue template for CS /2:1125
Atom OP2 is not in the residue template for GS /2:1126
Atom P is not in the residue template for CS /2:1127
Atom P is not in the residue template for CS /2:1128
Atom OP2 is not in the residue template for GS /2:1129
Atom OP2 is not in the residue template for GS /2:1130
Atom OP2 is not in the residue template for GS /2:1131
Atom P is not in the residue template for CS /2:1132
Atom OP2 is not in the residue template for AS /2:1133
Atom OP2 is not in the residue template for GS /2:1134
Atom P is not in the residue template for CS /2:1135
Atom P is not in the residue template for CS /2:1138
Atom P is not in the residue template for CS /2:1139
Atom OP2 is not in the residue template for GS /2:1140
Atom OP2 is not in the residue template for GS /2:1141
Atom OP2 is not in the residue template for GS /2:1142
Atom OP2 is not in the residue template for AS /2:1143
Atom OP2 is not in the residue template for AS /2:1144
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1146
Atom P is not in the residue template for CS /2:1147
Atom OP2 is not in the residue template for AS /2:1148
Atom OP2 is not in the residue template for AS /2:1149
Atom OP2 is not in the residue template for AS /2:1150
Atom OP2 is not in the residue template for GS /2:1151
Atom P is not in the residue template for CS /2:1153
Atom OP2 is not in the residue template for GS /2:1157
Atom OP2 is not in the residue template for GS /2:1158
Atom OP2 is not in the residue template for GS /2:1159
Atom P is not in the residue template for CS /2:1162
Atom P is not in the residue template for CS /2:1163
Atom OP2 is not in the residue template for GS /2:1164
Atom OP2 is not in the residue template for GS /2:1165
Atom OP2 is not in the residue template for GS /2:1166
Atom OP2 is not in the residue template for GS /2:1167
Atom OP2 is not in the residue template for GS /2:1168
7 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1180
Atom OP2 is not in the residue template for AS /2:1181
Atom OP2 is not in the residue template for AS /2:1182
Atom OP2 is not in the residue template for AS /2:1183
Atom OP2 is not in the residue template for GS /2:1184
Atom P is not in the residue template for CS /2:1185
Atom OP2 is not in the residue template for GS /2:1187
Atom OP2 is not in the residue template for AS /2:1188
Atom OP2 is not in the residue template for AS /2:1189
Atom OP2 is not in the residue template for AS /2:1190
Atom P is not in the residue template for CS /2:1191
Atom OP2 is not in the residue template for AS /2:1194
Atom OP2 is not in the residue template for AS /2:1195
Atom OP2 is not in the residue template for AS /2:1196
Atom OP2 is not in the residue template for GS /2:1197
Atom OP2 is not in the residue template for GS /2:1198
4 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1205
Atom OP2 is not in the residue template for GS /2:1206
Atom OP2 is not in the residue template for GS /2:1207
Atom OP2 is not in the residue template for AS /2:1208
Atom OP2 is not in the residue template for AS /2:1209
Atom OP2 is not in the residue template for GS /2:1210
2 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1213
Atom OP2 is not in the residue template for AS /2:1214
Atom P is not in the residue template for CS /2:1215
Atom P is not in the residue template for CS /2:1216
Atom OP2 is not in the residue template for AS /2:1217
Atom P is not in the residue template for CS /2:1218
Atom P is not in the residue template for CS /2:1219
Atom OP2 is not in the residue template for AS /2:1220
Atom OP2 is not in the residue template for GS /2:1221
Atom OP2 is not in the residue template for GS /2:1222
Atom OP2 is not in the residue template for AS /2:1223
Atom OP2 is not in the residue template for GS /2:1224
4 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1230
Atom P is not in the residue template for CS /2:1231
Atom OP2 is not in the residue template for GS /2:1233
Atom P is not in the residue template for CS /2:1234
Atom OP2 is not in the residue template for GS /2:1235
Atom OP2 is not in the residue template for GS /2:1236
Atom P is not in the residue template for CS /2:1237
Atom OP2 is not in the residue template for AS /2:1240
Atom OP2 is not in the residue template for AS /2:1241
Atom OP2 is not in the residue template for GS /2:1245
Atom OP2 is not in the residue template for AS /2:1246
Atom P is not in the residue template for CS /2:1247
Atom P is not in the residue template for CS /2:1249
Atom OP2 is not in the residue template for AS /2:1250
Atom OP2 is not in the residue template for AS /2:1251
Atom P is not in the residue template for CS /2:1252
Atom OP2 is not in the residue template for AS /2:1253
Atom P is not in the residue template for CS /2:1254
Atom OP2 is not in the residue template for GS /2:1255
Atom OP2 is not in the residue template for GS /2:1256
Atom OP2 is not in the residue template for GS /2:1257
Atom OP2 is not in the residue template for AS /2:1258
Atom OP2 is not in the residue template for AS /2:1259
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1261
Atom P is not in the residue template for CS /2:1262
Atom P is not in the residue template for CS /2:1264
Atom OP2 is not in the residue template for AS /2:1265
Atom P is not in the residue template for CS /2:1266
Atom P is not in the residue template for CS /2:1267
Atom P is not in the residue template for CS /2:1268
Atom OP2 is not in the residue template for GS /2:1269
Atom OP2 is not in the residue template for GS /2:1270
Atom P is not in the residue template for CS /2:1271
Atom P is not in the residue template for CS /2:1272
Atom P is not in the residue template for CS /2:1273
Atom OP2 is not in the residue template for GS /2:1274
Atom OP2 is not in the residue template for GS /2:1275
Atom OP2 is not in the residue template for AS /2:1276
Atom P is not in the residue template for CS /2:1277
Atom OP2 is not in the residue template for AS /2:1278
Atom P is not in the residue template for CS /2:1279
Atom OP2 is not in the residue template for GS /2:1280
Atom OP2 is not in the residue template for GS /2:1281
Atom OP2 is not in the residue template for AS /2:1282
Atom P is not in the residue template for CS /2:1283
Atom OP2 is not in the residue template for AS /2:1284
Atom OP2 is not in the residue template for GS /2:1285
Atom OP2 is not in the residue template for GS /2:1286
Atom OP2 is not in the residue template for AS /2:1287
Atom OP2 is not in the residue template for GS /2:1290
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1292
Atom OP2 is not in the residue template for AS /2:1293
Atom OP2 is not in the residue template for GS /2:1294
Atom OP2 is not in the residue template for AS /2:1295
Atom OP2 is not in the residue template for GS /2:1298
Atom OP2 is not in the residue template for AS /2:1299
2 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1303
Atom P is not in the residue template for CS /2:1305
Atom P is not in the residue template for CS /2:1309
Atom P is not in the residue template for CS /2:1311
Atom OP2 is not in the residue template for GS /2:1312
Atom OP2 is not in the residue template for AS /2:1313
Atom P is not in the residue template for CS /2:1316
Atom P is not in the residue template for CS /2:1317
Atom OP2 is not in the residue template for GS /2:1318
Atom OP2 is not in the residue template for GS /2:1320
Atom OP2 is not in the residue template for GS /2:1321
Atom OP2 is not in the residue template for GS /2:1322
Atom OP2 is not in the residue template for GS /2:1324
3 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1331
Atom OP2 is not in the residue template for AS /2:1332
Atom OP2 is not in the residue template for GS /2:1334
Atom OP2 is not in the residue template for GS /2:1335
Atom P is not in the residue template for CS /2:1336
Atom OP2 is not in the residue template for GS /2:1338
Atom P is not in the residue template for CS /2:1341
Atom OP2 is not in the residue template for AS /2:1344
Atom OP2 is not in the residue template for GS /2:1345
Atom OP2 is not in the residue template for GS /2:1348
Atom OP2 is not in the residue template for GS /2:1349
Atom OP2 is not in the residue template for GS /2:1351
3 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1355
Atom OP2 is not in the residue template for GS /2:1356
Atom OP2 is not in the residue template for AS /2:1357
Atom OP2 is not in the residue template for GS /2:1361
Atom P is not in the residue template for CS /2:1363
Atom OP2 is not in the residue template for GS /2:1365
Atom OP2 is not in the residue template for GS /2:1366
Atom OP2 is not in the residue template for AS /2:1369
Atom OP2 is not in the residue template for AS /2:1370
Atom P is not in the residue template for CS /2:1373
Atom P is not in the residue template for CS /2:1374
Atom OP2 is not in the residue template for GS /2:1375
Atom OP2 is not in the residue template for AS /2:1376
Atom OP2 is not in the residue template for AS /2:1378
Atom OP2 is not in the residue template for AS /2:1379
Atom P is not in the residue template for CS /2:1380
Atom OP2 is not in the residue template for GS /2:1381
Atom OP2 is not in the residue template for AS /2:1382
Atom P is not in the residue template for CS /2:1384
Atom OP2 is not in the residue template for GS /2:1385
Atom OP2 is not in the residue template for AS /2:1386
Atom OP2 is not in the residue template for GS /2:1387
Atom OP2 is not in the residue template for AS /2:1388
Atom P is not in the residue template for CS /2:1389
Atom OP2 is not in the residue template for GS /2:1393
Atom OP2 is not in the residue template for GS /2:1394
Atom P is not in the residue template for CS /2:1395
Atom OP2 is not in the residue template for AS /2:1396
Atom OP2 is not in the residue template for GS /2:1398
Atom P is not in the residue template for CS /2:1399
Atom OP2 is not in the residue template for AS /2:1401
Atom OP2 is not in the residue template for AS /2:1402
Atom P is not in the residue template for CS /2:1403
Atom OP2 is not in the residue template for AS /2:1405
Atom OP2 is not in the residue template for GS /2:1406
Atom OP2 is not in the residue template for AS /2:1409
Atom P is not in the residue template for CS /2:1410
Atom OP2 is not in the residue template for GS /2:1411
Atom P is not in the residue template for CS /2:1412
Atom OP2 is not in the residue template for GS /2:1413
Atom OP2 is not in the residue template for AS /2:1414
Atom P is not in the residue template for CS /2:1415
Atom P is not in the residue template for CS /2:1416
Atom P is not in the residue template for CS /2:1417
Atom OP2 is not in the residue template for GS /2:1424
Atom OP2 is not in the residue template for GS /2:1425
Atom P is not in the residue template for CS /2:1427
Atom OP2 is not in the residue template for GS /2:1428
Atom OP2 is not in the residue template for GS /2:1429
Atom P is not in the residue template for CS /2:1430
Atom OP2 is not in the residue template for GS /2:1431
Atom P is not in the residue template for CS /2:1433
Atom OP2 is not in the residue template for AS /2:1438
Atom OP2 is not in the residue template for AS /2:1439
Atom P is not in the residue template for CS /2:1440
Atom P is not in the residue template for CS /2:1443
Atom OP2 is not in the residue template for AS /2:1446
Atom OP2 is not in the residue template for AS /2:1448
Atom OP2 is not in the residue template for GS /2:1449
Atom OP2 is not in the residue template for GS /2:1450
Atom OP2 is not in the residue template for GS /2:1451
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1453
Atom OP2 is not in the residue template for AS /2:1454
Atom OP2 is not in the residue template for AS /2:1455
Atom OP2 is not in the residue template for GS /2:1456
Atom OP2 is not in the residue template for GS /2:1458
Atom OP2 is not in the residue template for GS /2:1459
Atom P is not in the residue template for CS /2:1460
Atom OP2 is not in the residue template for GS /2:1461
Atom P is not in the residue template for CS /2:1464
Atom OP2 is not in the residue template for AS /2:1465
Atom OP2 is not in the residue template for GS /2:1466
Atom P is not in the residue template for CS /2:1467
Atom P is not in the residue template for CS /2:1468
Atom OP2 is not in the residue template for AS /2:1469
Atom P is not in the residue template for CS /2:1470
Atom P is not in the residue template for CS /2:1471
Atom P is not in the residue template for CS /2:1472
Atom OP2 is not in the residue template for GS /2:1473
Atom OP2 is not in the residue template for AS /2:1474
Atom OP2 is not in the residue template for GS /2:1475
Atom OP2 is not in the residue template for AS /2:1476
Atom OP2 is not in the residue template for GS /2:1479
2 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1482
Atom OP2 is not in the residue template for AS /2:1483
Atom OP2 is not in the residue template for AS /2:1484
Atom OP2 is not in the residue template for AS /2:1486
Atom OP2 is not in the residue template for AS /2:1487
Atom P is not in the residue template for CS /2:1488
Atom OP2 is not in the residue template for AS /2:1489
Atom OP2 is not in the residue template for GS /2:1491
Atom P is not in the residue template for CS /2:1493
Atom OP2 is not in the residue template for GS /2:1495
Atom OP2 is not in the residue template for GS /2:1497
Atom OP2 is not in the residue template for AS /2:1498
Atom OP2 is not in the residue template for GS /2:1500
Atom P is not in the residue template for CS /2:1501
Atom P is not in the residue template for CS /2:1502
Atom P is not in the residue template for CS /2:1503
Atom OP2 is not in the residue template for AS /2:1506
Atom OP2 is not in the residue template for GS /2:1507
Atom OP2 is not in the residue template for AS /2:1508
Atom OP2 is not in the residue template for GS /2:1510
Atom P is not in the residue template for CS /2:1512
Atom P is not in the residue template for CS /2:1513
Atom OP2 is not in the residue template for GS /2:1514
Atom OP2 is not in the residue template for GS /2:1515
Atom OP2 is not in the residue template for GS /2:1516
Atom OP2 is not in the residue template for GS /2:1517
Atom P is not in the residue template for CS /2:1518
Atom OP2 is not in the residue template for GS /2:1520
Atom P is not in the residue template for CS /2:1521
Atom OP2 is not in the residue template for AS /2:1522
Atom P is not in the residue template for CS /2:1523
Atom OP2 is not in the residue template for GS /2:1524
Atom P is not in the residue template for CS /2:1525
Atom OP2 is not in the residue template for GS /2:1526
Atom P is not in the residue template for CS /2:1527
Atom OP2 is not in the residue template for GS /2:1528
Atom P is not in the residue template for CS /2:1529
Atom OP2 is not in the residue template for AS /2:1531
Atom P is not in the residue template for CS /2:1532
Atom OP2 is not in the residue template for AS /2:1533
Atom P is not in the residue template for CS /2:1534
Atom OP2 is not in the residue template for GS /2:1536
Atom OP2 is not in the residue template for AS /2:1537
Atom P is not in the residue template for CS /2:1538
Atom OP2 is not in the residue template for GS /2:1540
Atom OP2 is not in the residue template for GS /2:1541
Atom P is not in the residue template for CS /2:1542
Atom P is not in the residue template for CS /2:1544
Atom OP2 is not in the residue template for AS /2:1545
Atom OP2 is not in the residue template for GS /2:1546
Atom P is not in the residue template for CS /2:1547
Atom OP2 is not in the residue template for GS /2:1548
Atom OP2 is not in the residue template for GS /2:1550
Atom OP2 is not in the residue template for GS /2:1552
Atom P is not in the residue template for CS /2:1553
Atom P is not in the residue template for CS /2:1554
Atom OP2 is not in the residue template for AS /2:1556
Atom P is not in the residue template for CS /2:1557
Atom P is not in the residue template for CS /2:1558
Atom P is not in the residue template for CS /2:1559
Atom OP2 is not in the residue template for AS /2:1561
Atom P is not in the residue template for CS /2:1562
Atom OP2 is not in the residue template for GS /2:1563
Atom P is not in the residue template for CS /2:1564
Atom P is not in the residue template for CS /2:1565
Atom OP2 is not in the residue template for GS /2:1566
Atom OP2 is not in the residue template for GS /2:1567
Atom P is not in the residue template for CS /2:1568
Atom OP2 is not in the residue template for AS /2:1569
Atom OP2 is not in the residue template for GS /2:1570
Atom OP2 is not in the residue template for GS /2:1571
Atom P is not in the residue template for CS /2:1572
Atom OP2 is not in the residue template for GS /2:1573
Atom P is not in the residue template for CS /2:1574
Atom OP2 is not in the residue template for GS /2:1575
Atom OP2 is not in the residue template for GS /2:1576
Atom OP2 is not in the residue template for GS /2:1577
Atom OP2 is not in the residue template for AS /2:1579
Atom OP2 is not in the residue template for AS /2:1580
Atom P is not in the residue template for CS /2:1581
Atom P is not in the residue template for CS /2:1582
Atom P is not in the residue template for CS /2:1583
Atom OP2 is not in the residue template for GS /2:1584
Atom OP2 is not in the residue template for GS /2:1587
Atom OP2 is not in the residue template for AS /2:1588
Atom OP2 is not in the residue template for AS /2:1589
Atom P is not in the residue template for CS /2:1590
Atom P is not in the residue template for CS /2:1591
Atom P is not in the residue template for CS /2:1592
Atom P is not in the residue template for CS /2:1593
Atom OP2 is not in the residue template for AS /2:1594
Atom P is not in the residue template for CS /2:1597
Atom OP2 is not in the residue template for GS /2:1598
Atom OP2 is not in the residue template for GS /2:1600
Atom OP2 is not in the residue template for AS /2:1601
Atom OP2 is not in the residue template for GS /2:1603
Atom OP2 is not in the residue template for GS /2:1604
3 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1609
Atom OP2 is not in the residue template for GS /2:1610
Atom OP2 is not in the residue template for GS /2:1611
Atom OP2 is not in the residue template for GS /2:1612
Atom OP2 is not in the residue template for GS /2:1613
Atom OP2 is not in the residue template for AS /2:1614
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1618
Atom OP2 is not in the residue template for AS /2:1619
Atom OP2 is not in the residue template for AS /2:1620
Atom OP2 is not in the residue template for AS /2:1623
Atom P is not in the residue template for CS /2:1626
Atom P is not in the residue template for CS /2:1627
Atom P is not in the residue template for CS /2:1628
Atom P is not in the residue template for CS /2:1629
Atom OP2 is not in the residue template for AS /2:1630
Atom OP2 is not in the residue template for GS /2:1632
Atom OP2 is not in the residue template for AS /2:1633
Atom OP2 is not in the residue template for AS /2:1634
Atom P is not in the residue template for CS /2:1635
Atom OP2 is not in the residue template for GS /2:1636
Atom OP2 is not in the residue template for AS /2:1637
Atom OP2 is not in the residue template for GS /2:1638
Atom OP2 is not in the residue template for GS /2:1639
Atom OP2 is not in the residue template for AS /2:1640
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1644
Atom P is not in the residue template for CS /2:1645
Atom P is not in the residue template for CS /2:1646
Atom OP2 is not in the residue template for AS /2:1647
Atom OP2 is not in the residue template for GS /2:1648
Atom OP2 is not in the residue template for AS /2:1650
Atom OP2 is not in the residue template for AS /2:1651
Atom OP2 is not in the residue template for GS /2:1652
1 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1655
Atom OP2 is not in the residue template for GS /2:1656
Atom OP2 is not in the residue template for GS /2:1657
Atom OP2 is not in the residue template for GS /2:1658
Atom P is not in the residue template for CS /2:1660
Atom OP2 is not in the residue template for AS /2:1661
Atom OP2 is not in the residue template for AS /2:1663
Atom OP2 is not in the residue template for AS /2:1664
Atom OP2 is not in the residue template for GS /2:1665
Atom P is not in the residue template for CS /2:1666
Atom OP2 is not in the residue template for GS /2:1669
Atom P is not in the residue template for CS /2:1670
Atom OP2 is not in the residue template for GS /2:1671
Atom OP2 is not in the residue template for GS /2:1674
Atom OP2 is not in the residue template for AS /2:1675
Atom OP2 is not in the residue template for AS /2:1679
Atom OP2 is not in the residue template for GS /2:1680
Atom P is not in the residue template for CS /2:1682
Atom P is not in the residue template for CS /2:1683
Atom P is not in the residue template for CS /2:1684
Atom OP2 is not in the residue template for GS /2:1686
Atom P is not in the residue template for CS /2:1687
Atom P is not in the residue template for CS /2:1688
Atom P is not in the residue template for CS /2:1689
Atom OP2 is not in the residue template for GS /2:1693
Atom OP2 is not in the residue template for AS /2:1695
Atom P is not in the residue template for CS /2:1696
Atom OP2 is not in the residue template for AS /2:1697
Atom P is not in the residue template for CS /2:1698
Atom OP2 is not in the residue template for AS /2:1699
Atom P is not in the residue template for CS /2:1700
Atom P is not in the residue template for CS /2:1701
Atom OP2 is not in the residue template for GS /2:1702
Atom P is not in the residue template for CS /2:1704
Atom P is not in the residue template for CS /2:1705
Atom OP2 is not in the residue template for GS /2:1706
Atom P is not in the residue template for CS /2:1708
Atom OP2 is not in the residue template for GS /2:1709
Atom P is not in the residue template for CS /2:1710
Atom OP2 is not in the residue template for AS /2:1712
Atom P is not in the residue template for CS /2:1713
Atom OP2 is not in the residue template for AS /2:1715
Atom P is not in the residue template for CS /2:1716
Atom P is not in the residue template for CS /2:1717
Atom OP2 is not in the residue template for GS /2:1718
Atom OP2 is not in the residue template for AS /2:1719
Atom OP2 is not in the residue template for GS /2:1722
Atom OP2 is not in the residue template for GS /2:1723
Atom OP2 is not in the residue template for AS /2:1724
8 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1738
Atom P is not in the residue template for CS /2:1739
Atom P is not in the residue template for CS /2:1740
Atom P is not in the residue template for CS /2:1742
Atom OP2 is not in the residue template for GS /2:1743
Atom OP2 is not in the residue template for GS /2:1744
Atom OP2 is not in the residue template for AS /2:1745
Atom P is not in the residue template for CS /2:1747
Atom OP2 is not in the residue template for GS /2:1748
Atom OP2 is not in the residue template for GS /2:1749
Atom P is not in the residue template for CS /2:1750
Atom P is not in the residue template for CS /2:1751
Atom OP2 is not in the residue template for GS /2:1784
Atom P is not in the residue template for CS /2:1785
Atom OP2 is not in the residue template for GS /2:1787
Atom OP2 is not in the residue template for AS /2:1788
Atom OP2 is not in the residue template for GS /2:1789
Atom OP2 is not in the residue template for AS /2:1790
Atom OP2 is not in the residue template for AS /2:1791
2 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1794
Atom OP2 is not in the residue template for GS /2:1795
Atom OP2 is not in the residue template for GS /2:1796
Atom P is not in the residue template for CS /2:1798
Atom OP2 is not in the residue template for GS /2:1799
Atom OP2 is not in the residue template for AS /2:1800
Atom OP2 is not in the residue template for AS /2:1801
Atom P is not in the residue template for CS /2:1802
Atom OP2 is not in the residue template for GS /2:1805
Atom OP2 is not in the residue template for AS /2:1806
Atom P is not in the residue template for CS /2:1807
Atom OP2 is not in the residue template for AS /2:1809
Atom P is not in the residue template for CS /2:1811
Atom OP2 is not in the residue template for AS /2:1813
Atom OP2 is not in the residue template for GS /2:1814
Atom OP2 is not in the residue template for AS /2:1815
Atom OP2 is not in the residue template for GS /2:1816
Atom OP2 is not in the residue template for GS /2:1817
8 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1828
Atom OP2 is not in the residue template for GS /2:1829
Atom OP2 is not in the residue template for AS /2:1831
Atom P is not in the residue template for CS /2:1833
Atom OP2 is not in the residue template for AS /2:1834
Atom OP2 is not in the residue template for AS /2:1835
Atom OP2 is not in the residue template for GS /2:1836
Atom OP2 is not in the residue template for GS /2:1837
Atom P is not in the residue template for CS /2:1841
Atom OP2 is not in the residue template for GS /2:1843
Atom OP2 is not in the residue template for AS /2:1845
Atom OP2 is not in the residue template for GS /2:1846
Atom OP2 is not in the residue template for GS /2:1847
Atom OP2 is not in the residue template for GS /2:1849
Atom P is not in the residue template for CS /2:1852
Atom P is not in the residue template for CS /2:1853
Atom OP2 is not in the residue template for GS /2:1855
Atom P is not in the residue template for CS /2:1856
Atom OP2 is not in the residue template for GS /2:1857
Atom OP2 is not in the residue template for GS /2:1858
Atom OP2 is not in the residue template for AS /2:1859
Atom OP2 is not in the residue template for AS /2:1860
Atom OP2 is not in the residue template for GS /2:1861
2 messages similar to the above omitted
Atom P is not in the residue template for CS /2:1865
Atom OP2 is not in the residue template for AS /2:1866
Atom OP2 is not in the residue template for AS /2:1869
Unable to fetch template for 'B8NS': will connect using distance criteria
Unable to fetch template for '6MZS': will connect using distance criteria
Unable to fetch template for 'HYGS': will connect using distance criteria
Unable to fetch template for 'PUTS': will connect using distance criteria
Atom O5' is not in the residue template for CL /5:1
Atom P is not in the residue template for CL /5:3
Atom P is not in the residue template for AL /5:5
Atom P is not in the residue template for CL /5:6
Atom P is not in the residue template for CL /5:7
Atom P is not in the residue template for CL /5:9
1638 messages similar to the above omitted
Unable to fetch template for 'PUTL': will connect using distance criteria
Unable to fetch template for 'ANML': will connect using distance criteria
Unable to fetch template for '3HEL': will connect using distance criteria
Unable to fetch template for '6MZL': will connect using distance criteria
Unable to fetch template for 'UY1L': will connect using distance criteria
Atom P is not in the residue template for CL /7:3
Atom P is not in the residue template for AL /7:5
Atom P is not in the residue template for CL /7:6
Atom P is not in the residue template for CL /7:9
Atom P is not in the residue template for CL /7:10
50 messages similar to the above omitted
Atom O5' is not in the residue template for CL /8:1
Atom P is not in the residue template for AL /8:3
Atom P is not in the residue template for CL /8:4
Atom P is not in the residue template for CL /8:6
Atom P is not in the residue template for AL /8:9
Atom P is not in the residue template for CL /8:11
70 messages similar to the above omitted
Unable to fetch template for 'GDPC': will connect using distance criteria
Missing or incomplete sequence information. Inferred polymer connectivity.
notes | Fetching CCD AS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/AS/AS.cif
Fetching CCD CS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/CS/CS.cif
Fetching CCD GS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/GS/GS.cif
Chain information for
Class10_FR_EF2_merged_may20_real_space_refined_008-coot-0.cif #1
---
Chain | Description
2 | No description available
5 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
> close
> open
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-21.cif
Summary of feedback from opening
/yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-21.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 19
Unable to fetch template for '---': will connect using distance criteria
Unknown polymer entity '2' near line 229
Unknown polymer entity '84' near line 336
Unknown polymer entity '3' near line 345
Unknown polymer entity '85' near line 6724
Unknown polymer entity '4' near line 6752
99 messages similar to the above omitted
Skipping residue with duplicate label_seq_id -32767 in chain
Skipping residue with duplicate label_seq_id -32767 in chain
Skipping residue with duplicate label_seq_id -32767 in chain
Atom . is not in the residue template for LEU /CA:302
Atom . is not in the residue template for PRO /Lq:201
Atom . is not in the residue template for GLU /Lq:202
Atom . is not in the residue template for VAL /Lq:203
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for
Class10_FR_EF2_merged_may20_real_space_refined_008-coot-21.cif #1
---
Chain | Description
CA | No description available
CB | No description available
CC | No description available
CD | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lq | No description available
Lr | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> save
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1.pdb
> relModel #1
Chain IDs longer than 2 characters; truncating
QXcbConnection: XCB error: 3 (BadWindow), sequence: 23197, resource id:
9782191, major code: 40 (TranslateCoords), minor code: 0
> close
> open
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1.pdb
Chain information for
Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1.pdb #1
---
Chain | Description
CA | No description available
CB | No description available
CC | No description available
CD | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lq | No description available
Lr | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> close
> open
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1_KSRedit.pdb
Summary of feedback from opening
/yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1_KSRedit.pdb
---
warnings | CONECT record for nonexistent atom: 6619
PDB SEQRES record for chain LA is incomplete. Ignoring input sequence records
as basis for sequence.
PDB SEQRES record for chain LB is incomplete. Ignoring input sequence records
as basis for sequence.
PDB SEQRES record for chain LC is incomplete. Ignoring input sequence records
as basis for sequence.
PDB SEQRES record for chain LD is incomplete. Ignoring input sequence records
as basis for sequence.
PDB SEQRES record for chain LF is incomplete. Ignoring input sequence records
as basis for sequence.
59 messages similar to the above omitted
Chain information for
Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1_KSRedit.pdb #1
---
Chain | Description
CA | No description available
CB | No description available
CC | No description available
CD | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lq | No description available
Lr | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
> save
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1_KSRedit.cif
> relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> close
> open
> /yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1_KSRedit.cif
Summary of feedback from opening
/yonath_group/rajan/Human_RPS3/HCT15_polysome/Class10_EF2/Phenix/RealSpaceRefine_8/test/Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1_KSRedit.cif
---
warnings | Unknown polymer entity '2' near line 1522
Unknown polymer entity '4' near line 8362
Unknown polymer entity '5' near line 8938
Unknown polymer entity '8' near line 89271
Unknown polymer entity '9' near line 91178
75 messages similar to the above omitted
Atom . is not in the residue template for PRO /Lq:201
Atom . is not in the residue template for GLU /Lq:202
Atom . is not in the residue template for VAL /Lq:203
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for
Class10_FR_EF2_merged_may20_real_space_refined_008-coot-1_KSRedit.cif #1
---
Chain | Description
CA | No description available
CB | No description available
CC | No description available
CD | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lq | No description available
Lr | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SM | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 470.94
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:1.0
Manufacturer: ASUS
Model: System Product Name
OS: Rocky Linux 8.5 Green Obsidian
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 26Gi 20Gi 72Mi 16Gi 35Gi
Swap: 31Gi 0B 31Gi
Graphics:
07:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)
Subsystem: Gigabyte Technology Co., Ltd Device [1458:404c]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
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funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
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idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
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Jinja2: 3.1.2
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jupyter-core: 5.7.1
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kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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