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Opened 4 weeks ago
Last modified 3 weeks ago
#19131 assigned defect
Save mmCIF: not a legal chain id (underscore)
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-25-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202306232350 (2023-06-23 23:50:16 UTC)
Description
(Describe the actions that caused this problem to occur here)
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.dev202306232350 (2023-06-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/dell/Desktop/2510-SongPu/CVA6.A_particles.5XS4.cif
Summary of feedback from opening
/home/dell/Desktop/2510-SongPu/CVA6.A_particles.5XS4.cif
---
warnings | Unable to fetch template for ' VAL': might have incorrect bonds
Skipping atom "CA" near line 3799: missing coordinates
note | PDBx/mmCIF styling lost near line 3799. Rereading mmCIF file from the
beginning.
CVA6.A_particles.5XS4.cif title:
Structure of Coxsackievirus A6 (CVA6) virus A-particle [more info...]
Chain information for CVA6.A_particles.5XS4.cif #1
---
Chain | Description | UniProt
A A_10 A_11 A_12 A_13 A_14 A_15 A_16 A_17 A_18 A_19 A_2 A_20 A_21 A_22 A_23
A_24 A_25 A_26 A_27 A_28 A_29 A_3 A_30 A_31 A_32 A_33 A_34 A_35 A_36 A_37 A_38
A_39 A_4 A_40 A_41 A_42 A_43 A_44 A_45 A_46 A_47 A_48 A_49 A_5 A_50 A_51 A_52
A_53 A_54 A_55 A_56 A_57 A_58 A_59 A_6 A_60 A_7 A_8 A_9 | Genome polyprotein |
A0A0K2BNC7_9ENTO 1-305
B B_10 B_11 B_12 B_13 B_14 B_15 B_16 B_17 B_18 B_19 B_2 B_20 B_21 B_22 B_23
B_24 B_25 B_26 B_27 B_28 B_29 B_3 B_30 B_31 B_32 B_33 B_34 B_35 B_36 B_37 B_38
B_39 B_4 B_40 B_41 B_42 B_43 B_44 B_45 B_46 B_47 B_48 B_49 B_5 B_50 B_51 B_52
B_53 B_54 B_55 B_56 B_57 B_58 B_59 B_6 B_60 B_7 B_8 B_9 | Genome polyprotein |
A0A0K2BNC7_9ENTO 1-256
C C_10 C_11 C_12 C_13 C_14 C_15 C_16 C_17 C_18 C_19 C_2 C_20 C_21 C_22 C_23
C_24 C_25 C_26 C_27 C_28 C_29 C_3 C_30 C_31 C_32 C_33 C_34 C_35 C_36 C_37 C_38
C_39 C_4 C_40 C_41 C_42 C_43 C_44 C_45 C_46 C_47 C_48 C_49 C_5 C_50 C_51 C_52
C_53 C_54 C_55 C_56 C_57 C_58 C_59 C_6 C_60 C_7 C_8 C_9 | Genome polyprotein |
A0A0K2BNC7_9ENTO 1-240
> show surfaces
> show atoms
> hide atoms
> show cartoons
> hide surfaces
> dssp
> color bychain
> show surfaces
> hide surfaces
> show atoms
> style stick
Changed 294540 atom styles
> show surfaces
> hide surfaces
> color bypolymer
> show surfaces
> color #1 purple
> color #1 grey
> hide surfaces
> hide atoms
> show cartoons
> show atoms
> show surfaces
> hide surfaces
> style sphere
Changed 294540 atom styles
> style stick
Changed 294540 atom styles
> style ball
Changed 294540 atom styles
> style stick
Changed 294540 atom styles
> show surfaces
> open /home/dell/Desktop/2510-SongPu/cryosparc_P21_J119_005_volume_map.mrc
Opened cryosparc_P21_J119_005_volume_map.mrc as #2, grid size 700,700,700,
pixel 0.76, shown at step 1, values float32
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> color sel bypolymer
> volume #2 region 0,0,0,699,699,699 step 4
[Repeated 1 time(s)]
> volume #2 step 1
> select subtract #1
180 models selected
> transparency 50
> hide #!1 models
> transparency #2.2 0
> show #!1 models
> hide #!2 models
> transparency #1.2-181 0
> hide surfaces
> hide atoms
> show #!2 models
> ui mousemode right "translate selected models"
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> view matrix models #1,1,0,0,4.8985,0,1,0,12.312,0,0,1,7.03
> view matrix models #1,1,0,0,32.039,0,1,0,49.872,0,0,1,22.539
> view matrix models #1,1,0,0,39.739,0,1,0,46.882,0,0,1,34.684
> view matrix models #1,1,0,0,36.584,0,1,0,38.073,0,0,1,35.679
> select subtract #1
180 models selected
> ui mousemode right "rotate selected models"
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> view matrix models
> #1,0.99751,-0.065941,0.024928,46.672,0.020136,0.6054,0.79567,-58.428,-0.067559,-0.79318,0.60522,325.56
> transparency sel 50
> transparency sel 0
> select add #2
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 185 models
selected
> transparency sel 50
> select add #2
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 185 models
selected
> select add #2
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 185 models
selected
> select subtract #1
183 models selected
> select add #2
3 models selected
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 5 models selected
> select add #2
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 185 models
selected
> select subtract #1
183 models selected
> select extract #2
Expected an objects specifier or a keyword
> select subtract #2
Nothing selected
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> view matrix models
> #1,0.99827,0.031688,-0.049519,41.052,0.00025296,0.83998,0.54261,-49.845,0.058789,-0.54169,0.83852,184.5
> select subtract #1
180 models selected
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> view matrix models
> #1,0.99943,-0.0031351,-0.033752,45.209,0.020425,0.85036,0.52581,-53.042,0.027053,-0.5262,0.84993,185.63
> view matrix models
> #1,0.96895,0.13947,0.20417,-35.469,-0.2235,0.84722,0.48194,14.185,-0.10576,-0.51261,0.85209,212.71
> select subtract #1
180 models selected
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> view matrix models
> #1,0.81401,0.32981,0.47814,-106.7,-0.5167,0.78719,0.33667,129.29,-0.26535,-0.52111,0.81119,260.99
> select subtract #1
180 models selected
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule CVA6.A_particles.5XS4.cif (#1) to map
cryosparc_P21_J119_005_volume_map.mrc (#2) using 294540 atoms
average map value = 0.1039, steps = 92
shifted from previous position = 3.79
rotated from previous position = 2.81 degrees
atoms outside contour = 236535, contour level = 0.23258
Position of CVA6.A_particles.5XS4.cif (#1) relative to
cryosparc_P21_J119_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.80902410 0.30902702 0.49998231 -107.58701317
-0.50000724 0.80900437 0.30903832 123.43555027
-0.30898668 -0.50001423 0.80901978 266.91033269
Axis -0.57737450 0.57731486 -0.57736145
Axis point 0.00000000 547.88735347 -99.52182492
Rotation angle (degrees) 44.47762383
Shift along axis -20.72456039
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.80902,0.30903,0.49998,-105.61,-0.50001,0.809,0.30904,120.54,-0.30899,-0.50001,0.80902,269.02
> fitmap #1 inMap #2
Fit molecule CVA6.A_particles.5XS4.cif (#1) to map
cryosparc_P21_J119_005_volume_map.mrc (#2) using 294540 atoms
average map value = 0.1039, steps = 80
shifted from previous position = 4.1
rotated from previous position = 0.00199 degrees
atoms outside contour = 236530, contour level = 0.23258
Position of CVA6.A_particles.5XS4.cif (#1) relative to
cryosparc_P21_J119_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.80902700 0.30902173 0.49998089 -107.59313320
-0.49999167 0.80902339 0.30901372 123.43709121
-0.30900428 -0.49998672 0.80903006 266.89944713
Axis -0.57735082 0.57733992 -0.57736007
Axis point 99.53185212 448.38161682 0.00000000
Rotation angle (degrees) 44.47630748
Shift along axis -20.71293845
> select subtract #1
180 models selected
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> view matrix models
> #1,0.80903,0.30902,0.49998,-105.95,-0.49999,0.80902,0.30901,120.18,-0.309,-0.49999,0.80903,269.6
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.806,0.31154,0.5033,-106.59,-0.50208,0.81017,0.30256,121.89,-0.31349,-0.49656,0.80941,269.76
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.806,0.31154,0.5033,-106.7,-0.50208,0.81017,0.30256,124.28,-0.31349,-0.49656,0.80941,270.87
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.78803,0.32036,0.52572,-109.75,-0.52676,0.79285,0.30644,133.09,-0.31864,-0.51841,0.79355,280.77
> fitmap #1 inMap #2
Fit molecule CVA6.A_particles.5XS4.cif (#1) to map
cryosparc_P21_J119_005_volume_map.mrc (#2) using 294540 atoms
average map value = 0.1039, steps = 88
shifted from previous position = 4.2
rotated from previous position = 2.18 degrees
atoms outside contour = 236536, contour level = 0.23258
Position of CVA6.A_particles.5XS4.cif (#1) relative to
cryosparc_P21_J119_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.80902555 0.30901684 0.49998626 -107.59099512
-0.49999165 0.80902186 0.30901777 123.42653346
-0.30900812 -0.49999223 0.80902519 266.90309792
Axis -0.57735435 0.57734320 -0.57735327
Axis point 0.00000000 547.89945289 -99.51575058
Rotation angle (degrees) 44.47662869
Shift along axis -20.71977730
> select subtract #1
180 models selected
> ui mousemode right "translate selected models"
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> view matrix models
> #1,0.80903,0.30902,0.49999,-105.39,-0.49999,0.80902,0.30902,122.98,-0.30901,-0.49999,0.80903,270.77
> select subtract #1
180 models selected
> fitmap #1 inMap #2
Fit molecule CVA6.A_particles.5XS4.cif (#1) to map
cryosparc_P21_J119_005_volume_map.mrc (#2) using 294540 atoms
average map value = 0.1039, steps = 72
shifted from previous position = 4.46
rotated from previous position = 0.0027 degrees
atoms outside contour = 236507, contour level = 0.23258
Position of CVA6.A_particles.5XS4.cif (#1) relative to
cryosparc_P21_J119_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.80903980 0.30897423 0.49998954 -107.57869674
-0.49995457 0.80904127 0.30902695 123.41614065
-0.30903081 -0.49998715 0.80901966 266.92073145
Axis -0.57736908 0.57737353 -0.57730820
Axis point 547.92850879 0.00000000 448.36461289
Rotation angle (degrees) 44.47547827
Shift along axis -20.72569983
> volume #2 change image level -0.01229,0 level 0.285,0.8 level 0.5829,1
> volume #2 level 0.2192
> volume #2 level 0.23
> volume #2 level 0.2
> volume #2 level 0.15
> save /home/dell/Desktop/2510-SongPu/CVA6.pdb relModel #2
Chain IDs longer than 2 characters; truncating
> open /home/dell/Desktop/2510-SongPu/5FWW.cif
Summary of feedback from opening /home/dell/Desktop/2510-SongPu/5FWW.cif
---
warnings | Unable to fetch template for ' ALA': might have incorrect bonds
Skipping atom "CA" near line 4037: missing coordinates
notes | PDBx/mmCIF styling lost near line 4037. Rereading mmCIF file from the
beginning.
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
5FWW.cif title:
Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) [more
info...]
Chain information for 5FWW.cif #3
---
Chain | Description | UniProt
A | LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6 | LRP6_HUMAN 630-1246
B | KREMEN PROTEIN 1 | KREM1_HUMAN 30-322
C | DICKKOPF-RELATED PROTEIN 1 | DKK1_HUMAN 182-266
Non-standard residues in 5FWW.cif #3
---
CA — calcium ion
> select add #3
7730 atoms, 7934 bonds, 8 pseudobonds, 977 residues, 3 models selected
> color sel bypolymer
> select subtract #3
Nothing selected
> select add #3
7730 atoms, 7934 bonds, 8 pseudobonds, 977 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,98.329,0,1,0,249.38,0,0,1,58.623
> view matrix models #3,1,0,0,143.34,0,1,0,362.85,0,0,1,84.185
> view matrix models #3,1,0,0,174.14,0,1,0,384.56,0,0,1,158.85
> hide #3/A cartoons
> hide #3/C cartoons
> view matrix models #3,1,0,0,155.24,0,1,0,295.35,0,0,1,168.71
> view matrix models #3,1,0,0,156.98,0,1,0,293.06,0,0,1,170.29
> view matrix models #3,1,0,0,166.47,0,1,0,299.99,0,0,1,186.8
> hide #!1 models
> view matrix models #3,1,0,0,160.37,0,1,0,293.86,0,0,1,185.23
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.96811,-0.24434,-0.055301,163.82,0.22732,0.94956,-0.216,294.98,0.10529,0.19654,0.97483,182.59
> view matrix models
> #3,0.75388,-0.34641,0.55828,173.04,0.63654,0.17463,-0.75121,308.33,0.16274,0.92169,0.35215,157.83
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.75388,-0.34641,0.55828,165.75,0.63654,0.17463,-0.75121,290.39,0.16274,0.92169,0.35215,162.65
> view matrix models
> #3,0.75388,-0.34641,0.55828,172.94,0.63654,0.17463,-0.75121,313.35,0.16274,0.92169,0.35215,174.68
> view matrix models
> #3,0.75388,-0.34641,0.55828,164.19,0.63654,0.17463,-0.75121,304.83,0.16274,0.92169,0.35215,172.31
> view matrix models
> #3,0.75388,-0.34641,0.55828,165.43,0.63654,0.17463,-0.75121,313.02,0.16274,0.92169,0.35215,176.53
> view matrix models
> #3,0.75388,-0.34641,0.55828,163.96,0.63654,0.17463,-0.75121,315.37,0.16274,0.92169,0.35215,182.26
> view matrix models
> #3,0.75388,-0.34641,0.55828,158.39,0.63654,0.17463,-0.75121,318.69,0.16274,0.92169,0.35215,185.59
> view matrix models
> #3,0.75388,-0.34641,0.55828,157.72,0.63654,0.17463,-0.75121,314.53,0.16274,0.92169,0.35215,185.1
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.6507,-0.28649,0.70321,157.29,0.75929,0.23532,-0.60672,317.95,0.0083392,0.92874,0.37065,182.63
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.6507,-0.28649,0.70321,154.55,0.75929,0.23532,-0.60672,318.28,0.0083392,0.92874,0.37065,180.36
> fitmap #3 inMap #2
Fit molecule 5FWW.cif (#3) to map cryosparc_P21_J119_005_volume_map.mrc (#2)
using 7730 atoms
average map value = 0.04119, steps = 260
shifted from previous position = 15.7
rotated from previous position = 20.1 degrees
atoms outside contour = 6887, contour level = 0.15
Position of 5FWW.cif (#3) relative to cryosparc_P21_J119_005_volume_map.mrc
(#2) coordinates:
Matrix rotation and translation
0.85176036 -0.17945428 0.49224024 156.11585607
0.51852879 0.15415638 -0.84104917 306.68156297
0.07504789 0.97161308 0.22435651 176.85729999
Axis 0.91239888 0.20999270 0.35132798
Axis point 0.00000000 84.70899014 212.29206443
Rotation angle (degrees) 83.38849461
Shift along axis 268.97573922
> volume #2 level 0.1
> select subtract #3
Nothing selected
> style #!3 stick
Changed 7730 atom styles
> show #!3 atoms
> hide #3/C cartoons
> hide #3/C
> hide #3/A
> ui mousemode right "rotate selected models"
> select add #3
7730 atoms, 7934 bonds, 8 pseudobonds, 977 residues, 3 models selected
> view matrix models
> #3,0.8673,0.093936,0.48885,150.85,0.47696,0.1243,-0.87009,305.99,-0.14249,0.98779,0.062998,169.85
> view matrix models
> #3,0.48705,-0.46014,0.74233,159.27,-0.76744,0.18025,0.61526,306.73,-0.41691,-0.86936,-0.26533,196.81
> fitmap #3 inMap #2
Fit molecule 5FWW.cif (#3) to map cryosparc_P21_J119_005_volume_map.mrc (#2)
using 7730 atoms
average map value = 0.06892, steps = 136
shifted from previous position = 13.1
rotated from previous position = 12.9 degrees
atoms outside contour = 5756, contour level = 0.1
Position of 5FWW.cif (#3) relative to cryosparc_P21_J119_005_volume_map.mrc
(#2) coordinates:
Matrix rotation and translation
0.61161359 -0.46120504 0.64282090 160.80978086
-0.73581856 -0.03306841 0.67637084 317.03849085
-0.29068857 -0.88667716 -0.35958832 203.20261260
Axis -0.84893470 0.50701488 -0.14915022
Axis point 0.00000000 285.42098168 -37.35006150
Rotation angle (degrees) 112.98695726
Shift along axis -6.08148514
> view matrix models
> #3,0.7145,0.10314,0.69199,152.14,-0.61814,-0.37023,0.69342,326.38,0.32771,-0.9232,-0.20078,218.26
> view matrix models
> #3,0.51704,0.14752,0.84315,150.13,-0.81174,-0.22801,0.53767,317.18,0.27156,-0.96242,0.001858,221.49
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.51704,0.14752,0.84315,142.22,-0.81174,-0.22801,0.53767,312.18,0.27156,-0.96242,0.001858,217.79
> hide sel atoms
> view matrix models
> #3,0.51704,0.14752,0.84315,144.63,-0.81174,-0.22801,0.53767,315.78,0.27156,-0.96242,0.001858,217.87
> view matrix models
> #3,0.51704,0.14752,0.84315,152.1,-0.81174,-0.22801,0.53767,360.58,0.27156,-0.96242,0.001858,180.68
> show #!1 models
> hide #!1 models
> view matrix models
> #3,0.51704,0.14752,0.84315,155.23,-0.81174,-0.22801,0.53767,316.15,0.27156,-0.96242,0.001858,205.61
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.056074,0.1482,0.98737,147.93,-0.29493,0.94233,-0.15819,288.93,-0.95387,-0.30007,-0.0091315,170.9
> view matrix models
> #3,0.083174,-0.095794,0.99192,155.36,-0.96595,0.23695,0.10388,296.39,-0.24499,-0.96679,-0.072824,195.51
> view matrix models
> #3,-0.73368,-0.59291,0.33191,139.81,-0.67898,0.62081,-0.39189,284.76,0.026305,-0.51288,-0.85805,177.08
> view matrix models
> #3,-0.52927,-0.66854,0.52243,148.22,-0.84841,0.41064,-0.33404,287.15,0.0087893,-0.62003,-0.78453,180.26
> view matrix models
> #3,-0.56579,-0.76394,0.31029,145.79,-0.82162,0.49066,-0.29017,286.75,0.069425,-0.41911,-0.90528,175.08
> view matrix models
> #3,-0.62783,-0.70976,0.31947,143.79,-0.75859,0.64987,-0.04701,288.88,-0.17425,-0.27186,-0.94643,167.17
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.62783,-0.70976,0.31947,145.39,-0.75859,0.64987,-0.04701,288.67,-0.17425,-0.27186,-0.94643,173.04
> view matrix models
> #3,-0.62783,-0.70976,0.31947,137.12,-0.75859,0.64987,-0.04701,281.33,-0.17425,-0.27186,-0.94643,169.5
> view matrix models
> #3,-0.62783,-0.70976,0.31947,124.32,-0.75859,0.64987,-0.04701,295.03,-0.17425,-0.27186,-0.94643,170.91
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.14056,-0.42903,0.89229,137.08,-0.61732,0.74258,0.2598,300.98,-0.77406,-0.51431,-0.36922,175.73
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.076992,-0.45609,0.8866,138.69,-0.54621,0.76322,0.34519,303.01,-0.83411,-0.45769,-0.30788,174.35
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.076992,-0.45609,0.8866,141.61,-0.54621,0.76322,0.34519,303.44,-0.83411,-0.45769,-0.30788,169.85
> view matrix models
> #3,-0.076992,-0.45609,0.8866,134.55,-0.54621,0.76322,0.34519,303.45,-0.83411,-0.45769,-0.30788,170.97
> fitmap #3 inMap #2
Fit molecule 5FWW.cif (#3) to map cryosparc_P21_J119_005_volume_map.mrc (#2)
using 7730 atoms
average map value = 0.0308, steps = 248
shifted from previous position = 21.6
rotated from previous position = 25.5 degrees
atoms outside contour = 6829, contour level = 0.1
Position of 5FWW.cif (#3) relative to cryosparc_P21_J119_005_volume_map.mrc
(#2) coordinates:
Matrix rotation and translation
0.33748663 -0.45360691 0.82482940 147.24542568
-0.61984521 0.55237011 0.55738601 309.29833367
-0.70844526 -0.69937688 -0.09474855 191.92254353
Axis -0.63170512 0.77069227 -0.08355879
Axis point 319.05630734 0.00000000 -21.28840518
Rotation angle (degrees) 95.88003400
Shift along axis 129.32132965
> hide #!3 models
> color #1 black
> show #!1 models
> color #1 grey
> volume #2 level 0.15
> volume #2 level 0.18
> open /home/dell/Desktop/2510-SongPu/cryosparc_P21_J121_005_volume_map.mrc
File size 726663168 too small for grid size (700,700,700)
> open /home/dell/Desktop/2510-SongPu/cryosparc_P21_J121_005_volume_map.mrc
Opened cryosparc_P21_J121_005_volume_map.mrc as #4, grid size 700,700,700,
pixel 0.76, shown at step 1, values float32
> hide #!2 models
> volume #4 region 0,0,0,699,699,699 step 4
[Repeated 1 time(s)]
> volume #4 step 1
> transparency #1.2-181#4.2 50
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> transparency #2.2#4.2 0
> transparency #2.2#4.2 50
> select add #2
7730 atoms, 7934 bonds, 8 pseudobonds, 977 residues, 6 models selected
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select subtract #3
3 models selected
> select add #2
3 models selected
> clear sel
Unknown command: clear sel
> select subtract #2
Nothing selected
> color #4 #c0bfbcff models
> transparency #1.2-181#4.2 0
> select add #4
3 models selected
> transparency sel 50
> select add #4
3 models selected
> select add #4
3 models selected
> select ~sel & ##selected
Nothing selected
> select subtract #4
Nothing selected
> select add #2
3 models selected
> select add #2
3 models selected
> select ~sel & ##selected
Nothing selected
> select subtract #2
Nothing selected
> select add #1
294540 atoms, 303120 bonds, 360 pseudobonds, 37560 residues, 2 models selected
> color sel bypolymer
> select subtract #1
180 models selected
> close #2
> fitmap #1 inMap #4
Fit molecule CVA6.A_particles.5XS4.cif (#1) to map
cryosparc_P21_J121_005_volume_map.mrc (#4) using 294540 atoms
average map value = 0.1044, steps = 24
shifted from previous position = 0.00239
rotated from previous position = 0.00227 degrees
atoms outside contour = 238503, contour level = 0.25318
Position of CVA6.A_particles.5XS4.cif (#1) relative to
cryosparc_P21_J121_005_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.80904475 0.30899464 0.49996891 -107.57968326
-0.49996893 0.80902570 0.30904448 123.42141241
-0.30899460 -0.49999973 0.80902571 266.91385844
Axis -0.57738865 0.57733106 -0.57733110
Axis point 0.00000000 547.90223893 -99.50903893
Rotation angle (degrees) 44.47566489
Shift along axis -20.72736894
> fitmap #1 inMap #4
Fit molecule CVA6.A_particles.5XS4.cif (#1) to map
cryosparc_P21_J121_005_volume_map.mrc (#4) using 294540 atoms
average map value = 0.1044, steps = 24
shifted from previous position = 0.00866
rotated from previous position = 0.00159 degrees
atoms outside contour = 238512, contour level = 0.25318
Position of CVA6.A_particles.5XS4.cif (#1) relative to
cryosparc_P21_J121_005_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.80903593 0.30901580 0.49997010 -107.59005276
-0.49999149 0.80901109 0.30904623 123.43434501
-0.30898119 -0.50001029 0.80902431 266.91344339
Axis -0.57738701 0.57731192 -0.57735188
Axis point 0.00000000 547.89809192 -99.51522570
Rotation angle (degrees) 44.47668019
Shift along axis -20.72175988
> volume #4 level 0.2
> volume #4 change image level -0.01343,0 level 0.325,0.8 level 0.649,1
> volume #4 level 0.15
> volume #4 level 0.13
> color #1 grey
> show #!3 models
> select add #3
7730 atoms, 7934 bonds, 8 pseudobonds, 977 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.33749,-0.45361,0.82483,145.04,-0.61985,0.55237,0.55739,306.5,-0.70845,-0.69938,-0.094749,192.81
> view matrix models
> #3,0.33749,-0.45361,0.82483,143.49,-0.61985,0.55237,0.55739,303.64,-0.70845,-0.69938,-0.094749,193.92
> view matrix models
> #3,0.33749,-0.45361,0.82483,145.75,-0.61985,0.55237,0.55739,309.66,-0.70845,-0.69938,-0.094749,188.16
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.089883,-0.32819,0.94032,137.06,-0.56032,0.79722,0.22469,301.49,-0.82339,-0.50669,-0.25555,180.14
> view matrix models
> #3,0.088053,-0.41203,0.9069,141.49,-0.5454,0.74191,0.39002,305.06,-0.83354,-0.52896,-0.15939,181.68
> view matrix models
> #3,0.22721,-0.45253,0.86232,144.22,-0.55112,0.6703,0.49697,307.79,-0.8029,-0.58815,-0.0971,184.23
> view matrix models
> #3,-0.30082,-0.2045,0.9315,130.69,-0.24392,0.96075,0.13215,302.8,-0.92196,-0.18746,-0.33889,170.98
> view matrix models
> #3,-0.062534,0.0022573,0.99804,131.87,-0.11741,0.99304,-0.0096027,302.57,-0.99111,-0.11778,-0.061833,172.07
> ui mousemode right "move picked models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.069238,0.052889,0.9962,130.39,-0.54668,0.83329,-0.082236,302.49,-0.83447,-0.5503,-0.028781,185.76
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.069238,0.052889,0.9962,123.71,-0.54668,0.83329,-0.082236,292.62,-0.83447,-0.5503,-0.028781,187.14
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.076866,0.074518,0.99425,124.11,-0.528,0.84894,-0.022808,293.51,-0.84576,-0.52321,0.1046,188.97
> view matrix models
> #3,0.069213,0.066942,0.99535,124.29,-0.59431,0.80414,-0.012756,294.47,-0.80126,-0.59066,0.095441,190.96
> view matrix models
> #3,0.034486,0.045672,0.99836,124.69,-0.67438,0.73831,-0.010481,295.77,-0.73758,-0.67291,0.056262,192.9
> view matrix models
> #3,-0.30239,0.57405,0.76094,103.02,-0.55294,0.54462,-0.63059,289.62,-0.77641,-0.61144,0.15272,192.85
> view matrix models
> #3,-0.32049,0.51415,0.79557,105.23,0.042615,0.84685,-0.53013,287.51,-0.94629,-0.136,-0.29332,169.67
> undo
[Repeated 1 time(s)]
> view matrix models
> #3,0.25131,0.12505,0.95979,123.27,-0.70394,0.7042,0.09257,298.55,-0.66431,-0.6989,0.265,198.28
> view matrix models
> #3,-0.36869,0.79102,0.48822,91.15,-0.59269,0.20457,-0.77902,295.76,-0.71609,-0.57658,0.39341,197.1
> view matrix models
> #3,-0.45868,0.73388,0.50104,92.342,-0.732,0.0076091,-0.68127,302.14,-0.50378,-0.67924,0.5337,204.22
> view matrix models
> #3,-0.27063,0.92895,0.25263,83.355,-0.96,-0.24085,-0.14278,318.09,-0.071789,-0.28116,0.95697,204.74
> view matrix models
> #3,-0.71403,0.69832,0.050166,82.544,-0.68535,-0.68253,-0.25388,329.99,-0.14305,-0.21566,0.96593,202.6
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.71403,0.69832,0.050166,75.573,-0.68535,-0.68253,-0.25388,338.82,-0.14305,-0.21566,0.96593,200.69
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.80156,0.59779,-0.012058,76.485,-0.57408,-0.77509,-0.26394,341.96,-0.16713,-0.20465,0.96446,200.19
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.80156,0.59779,-0.012058,75.316,-0.57408,-0.77509,-0.26394,344.93,-0.16713,-0.20465,0.96446,199.61
> view matrix models
> #3,-0.80156,0.59779,-0.012058,76.123,-0.57408,-0.77509,-0.26394,346.09,-0.16713,-0.20465,0.96446,199.45
> view matrix models
> #3,-0.80156,0.59779,-0.012058,77.969,-0.57408,-0.77509,-0.26394,347.58,-0.16713,-0.20465,0.96446,202.23
> view matrix models
> #3,-0.80156,0.59779,-0.012058,77.085,-0.57408,-0.77509,-0.26394,349.47,-0.16713,-0.20465,0.96446,203.46
> view matrix models
> #3,-0.80156,0.59779,-0.012058,78.389,-0.57408,-0.77509,-0.26394,350.53,-0.16713,-0.20465,0.96446,204.65
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.79109,0.61085,-0.032214,77.703,-0.58087,-0.76668,-0.27348,350.06,-0.19175,-0.19764,0.96134,204.22
> view matrix models
> #3,-0.71459,0.6835,-0.14896,73.919,-0.6141,-0.7149,-0.33437,347.18,-0.33504,-0.14746,0.93059,201.22
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.65123,0.68124,-0.33437,70.74,-0.74496,-0.6579,0.11051,353.54,-0.1447,0.32106,0.93594,189.76
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.71459,0.6835,-0.14896,74.781,-0.6141,-0.7149,-0.33437,346.45,-0.33504,-0.14746,0.93059,198.79
> fitmap #3 inMap #4
Fit molecule 5FWW.cif (#3) to map cryosparc_P21_J121_005_volume_map.mrc (#4)
using 7730 atoms
average map value = 0.005442, steps = 448
shifted from previous position = 1.26
rotated from previous position = 2.08 degrees
atoms outside contour = 7560, contour level = 0.13
Position of 5FWW.cif (#3) relative to cryosparc_P21_J121_005_volume_map.mrc
(#4) coordinates:
Matrix rotation and translation
-0.73279646 0.66838131 -0.12757646 75.50974970
-0.59776900 -0.72191462 -0.34858496 344.92530980
-0.32508699 -0.17918057 0.92855412 199.58331348
Axis 0.13105591 0.15279959 -0.97952878
Axis point 119.44853121 170.64104437 0.00000000
Rotation angle (degrees) 139.73634720
Shift along axis -132.89715497
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.7328,0.66838,-0.12758,77.022,-0.59777,-0.72191,-0.34858,342.59,-0.32509,-0.17918,0.92855,206.92
> view matrix models
> #3,-0.7328,0.66838,-0.12758,80.511,-0.59777,-0.72191,-0.34858,345.95,-0.32509,-0.17918,0.92855,196.9
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.69545,0.61691,0.36847,92.064,-0.71813,-0.57873,-0.38647,340.4,-0.02517,-0.53338,0.8455,207.13
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.56707,-0.54409,-0.61839,105.32,0.43705,-0.83512,0.334,369.97,-0.69815,-0.080865,0.71137,187.23
> view matrix models
> #3,0.66398,-0.37275,-0.64822,108.72,-0.15878,0.77684,-0.60935,302.57,0.7307,0.50752,0.45662,176.06
> view matrix models
> #3,0.28014,-0.01651,-0.95982,89.987,-0.30041,0.94812,-0.10399,306.9,0.91174,0.31747,0.26065,178.68
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.42013,-0.43109,-0.79853,99.665,0.7596,0.31437,-0.56936,322.6,0.49648,-0.84577,0.19539,206.49
> undo
> ui mousemode right "translate selected atoms"
> fitmap #3 inMap #4
Fit molecule 5FWW.cif (#3) to map cryosparc_P21_J121_005_volume_map.mrc (#4)
using 7730 atoms
average map value = 0.1021, steps = 224
shifted from previous position = 9.22
rotated from previous position = 14.3 degrees
atoms outside contour = 5367, contour level = 0.13
Position of 5FWW.cif (#3) relative to cryosparc_P21_J121_005_volume_map.mrc
(#4) coordinates:
Matrix rotation and translation
0.27942005 0.04731800 -0.95900231 93.62413080
-0.52452983 0.84410142 -0.11118113 309.82985549
0.80423435 0.53409156 0.26067856 184.24219239
Axis 0.32875937 -0.89834978 -0.29135021
Axis point 38.27758390 0.00000000 172.13287570
Rotation angle (degrees) 78.92463595
Shift along axis -301.23477378
> show sel atoms
> hide sel atoms
> save /home/dell/Desktop/2510-SongPu/CVA6.pdb models #1 relModel #4
Chain IDs longer than 2 characters; truncating
> save /home/dell/Desktop/2510-SongPu/kremen-mono.pdb models #3 relModel #4
> info #3
3 models
#3, 5FWW.cif, shown
7730 atoms, 7934 bonds, 977 residues, 3 chains (A,B,C)
5 metal coordination bonds, 3 missing structure
#3.1, metal coordination bonds, shown, 5 pseudobonds
#3.2, missing structure, shown, 3 pseudobonds
> info #1
182 models
#1, CVA6.A_particles.5XS4.cif, shown
294540 atoms, 303120 bonds, 37560 residues, 180 chains
(A,B,C,A_2,B_2,C_2,A_3,B_3,C_3,A_4,B_4,C_4,A_5,B_5,C_5,A_6,B_6,C_6,A_7,B_7,C_7,A_8,B_8,C_8,A_9,B_9,C_9,A_10,B_10,C_10,A_11,B_11,C_11,A_12,B_12,C_12,A_13,B_13,C_13,A_14,B_14,C_14,A_15,B_15,C_15,A_16,B_16,C_16,A_17,B_17,C_17,A_18,B_18,C_18,A_19,B_19,C_19,A_20,B_20,C_20,A_21,B_21,C_21,A_22,B_22,C_22,A_23,B_23,C_23,A_24,B_24,C_24,A_25,B_25,C_25,A_26,B_26,C_26,A_27,B_27,C_27,A_28,B_28,C_28,A_29,B_29,C_29,A_30,B_30,C_30,A_31,B_31,C_31,A_32,B_32,C_32,A_33,B_33,C_33,A_34,B_34,C_34,A_35,B_35,C_35,A_36,B_36,C_36,A_37,B_37,C_37,A_38,B_38,C_38,A_39,B_39,C_39,A_40,B_40,C_40,A_41,B_41,C_41,A_42,B_42,C_42,A_43,B_43,C_43,A_44,B_44,C_44,A_45,B_45,C_45,A_46,B_46,C_46,A_47,B_47,C_47,A_48,B_48,C_48,A_49,B_49,C_49,A_50,B_50,C_50,A_51,B_51,C_51,A_52,B_52,C_52,A_53,B_53,C_53,A_54,B_54,C_54,A_55,B_55,C_55,A_56,B_56,C_56,A_57,B_57,C_57,A_58,B_58,C_58,A_59,B_59,C_59,A_60,B_60,C_60)
360 missing structure
#1.1, missing structure, shown, 360 pseudobonds
#1.2, CVA6.A_particles.5XS4.cif_A SES surface, shown, 229356 triangles
#1.3, CVA6.A_particles.5XS4.cif_A_10 SES surface, shown, 230076 triangles
#1.4, CVA6.A_particles.5XS4.cif_A_11 SES surface, shown, 229854 triangles
#1.5, CVA6.A_particles.5XS4.cif_A_12 SES surface, shown, 229572 triangles
#1.6, CVA6.A_particles.5XS4.cif_A_13 SES surface, shown, 229434 triangles
#1.7, CVA6.A_particles.5XS4.cif_A_14 SES surface, shown, 229978 triangles
#1.8, CVA6.A_particles.5XS4.cif_A_15 SES surface, shown, 229652 triangles
#1.9, CVA6.A_particles.5XS4.cif_A_16 SES surface, shown, 230718 triangles
#1.10, CVA6.A_particles.5XS4.cif_A_17 SES surface, shown, 230326 triangles
#1.11, CVA6.A_particles.5XS4.cif_A_18 SES surface, shown, 230720 triangles
#1.12, CVA6.A_particles.5XS4.cif_A_19 SES surface, shown, 229878 triangles
#1.13, CVA6.A_particles.5XS4.cif_A_2 SES surface, shown, 230076 triangles
#1.14, CVA6.A_particles.5XS4.cif_A_20 SES surface, shown, 228428 triangles
#1.15, CVA6.A_particles.5XS4.cif_A_21 SES surface, shown, 231044 triangles
#1.16, CVA6.A_particles.5XS4.cif_A_22 SES surface, shown, 231394 triangles
#1.17, CVA6.A_particles.5XS4.cif_A_23 SES surface, shown, 231068 triangles
#1.18, CVA6.A_particles.5XS4.cif_A_24 SES surface, shown, 229504 triangles
#1.19, CVA6.A_particles.5XS4.cif_A_25 SES surface, shown, 229964 triangles
#1.20, CVA6.A_particles.5XS4.cif_A_26 SES surface, shown, 231544 triangles
#1.21, CVA6.A_particles.5XS4.cif_A_27 SES surface, shown, 231334 triangles
#1.22, CVA6.A_particles.5XS4.cif_A_28 SES surface, shown, 229508 triangles
#1.23, CVA6.A_particles.5XS4.cif_A_29 SES surface, shown, 230160 triangles
#1.24, CVA6.A_particles.5XS4.cif_A_3 SES surface, shown, 229862 triangles
#1.25, CVA6.A_particles.5XS4.cif_A_30 SES surface, shown, 230910 triangles
#1.26, CVA6.A_particles.5XS4.cif_A_31 SES surface, shown, 229956 triangles
#1.27, CVA6.A_particles.5XS4.cif_A_32 SES surface, shown, 229150 triangles
#1.28, CVA6.A_particles.5XS4.cif_A_33 SES surface, shown, 230772 triangles
#1.29, CVA6.A_particles.5XS4.cif_A_34 SES surface, shown, 230784 triangles
#1.30, CVA6.A_particles.5XS4.cif_A_35 SES surface, shown, 230214 triangles
#1.31, CVA6.A_particles.5XS4.cif_A_36 SES surface, shown, 229284 triangles
#1.32, CVA6.A_particles.5XS4.cif_A_37 SES surface, shown, 230646 triangles
#1.33, CVA6.A_particles.5XS4.cif_A_38 SES surface, shown, 230930 triangles
#1.34, CVA6.A_particles.5XS4.cif_A_39 SES surface, shown, 230076 triangles
#1.35, CVA6.A_particles.5XS4.cif_A_4 SES surface, shown, 229932 triangles
#1.36, CVA6.A_particles.5XS4.cif_A_40 SES surface, shown, 230030 triangles
#1.37, CVA6.A_particles.5XS4.cif_A_41 SES surface, shown, 229546 triangles
#1.38, CVA6.A_particles.5XS4.cif_A_42 SES surface, shown, 229934 triangles
#1.39, CVA6.A_particles.5XS4.cif_A_43 SES surface, shown, 230860 triangles
#1.40, CVA6.A_particles.5XS4.cif_A_44 SES surface, shown, 231180 triangles
#1.41, CVA6.A_particles.5XS4.cif_A_45 SES surface, shown, 231162 triangles
#1.42, CVA6.A_particles.5XS4.cif_A_46 SES surface, shown, 230166 triangles
#1.43, CVA6.A_particles.5XS4.cif_A_47 SES surface, shown, 230620 triangles
#1.44, CVA6.A_particles.5XS4.cif_A_48 SES surface, shown, 229838 triangles
#1.45, CVA6.A_particles.5XS4.cif_A_49 SES surface, shown, 228398 triangles
#1.46, CVA6.A_particles.5XS4.cif_A_5 SES surface, shown, 229450 triangles
#1.47, CVA6.A_particles.5XS4.cif_A_50 SES surface, shown, 230746 triangles
#1.48, CVA6.A_particles.5XS4.cif_A_51 SES surface, shown, 229600 triangles
#1.49, CVA6.A_particles.5XS4.cif_A_52 SES surface, shown, 229550 triangles
#1.50, CVA6.A_particles.5XS4.cif_A_53 SES surface, shown, 229962 triangles
#1.51, CVA6.A_particles.5XS4.cif_A_54 SES surface, shown, 229776 triangles
#1.52, CVA6.A_particles.5XS4.cif_A_55 SES surface, shown, 229964 triangles
#1.53, CVA6.A_particles.5XS4.cif_A_56 SES surface, shown, 230776 triangles
#1.54, CVA6.A_particles.5XS4.cif_A_57 SES surface, shown, 230038 triangles
#1.55, CVA6.A_particles.5XS4.cif_A_58 SES surface, shown, 229998 triangles
#1.56, CVA6.A_particles.5XS4.cif_A_59 SES surface, shown, 229580 triangles
#1.57, CVA6.A_particles.5XS4.cif_A_6 SES surface, shown, 230732 triangles
#1.58, CVA6.A_particles.5XS4.cif_A_60 SES surface, shown, 230624 triangles
#1.59, CVA6.A_particles.5XS4.cif_A_7 SES surface, shown, 230120 triangles
#1.60, CVA6.A_particles.5XS4.cif_A_8 SES surface, shown, 228398 triangles
#1.61, CVA6.A_particles.5XS4.cif_A_9 SES surface, shown, 230604 triangles
#1.62, CVA6.A_particles.5XS4.cif_B SES surface, shown, 191076 triangles
#1.63, CVA6.A_particles.5XS4.cif_B_10 SES surface, shown, 191984 triangles
#1.64, CVA6.A_particles.5XS4.cif_B_11 SES surface, shown, 192858 triangles
#1.65, CVA6.A_particles.5XS4.cif_B_12 SES surface, shown, 190932 triangles
#1.66, CVA6.A_particles.5XS4.cif_B_13 SES surface, shown, 191118 triangles
#1.67, CVA6.A_particles.5XS4.cif_B_14 SES surface, shown, 191522 triangles
#1.68, CVA6.A_particles.5XS4.cif_B_15 SES surface, shown, 191948 triangles
#1.69, CVA6.A_particles.5XS4.cif_B_16 SES surface, shown, 192136 triangles
#1.70, CVA6.A_particles.5XS4.cif_B_17 SES surface, shown, 191904 triangles
#1.71, CVA6.A_particles.5XS4.cif_B_18 SES surface, shown, 191994 triangles
#1.72, CVA6.A_particles.5XS4.cif_B_19 SES surface, shown, 191352 triangles
#1.73, CVA6.A_particles.5XS4.cif_B_2 SES surface, shown, 191684 triangles
#1.74, CVA6.A_particles.5XS4.cif_B_20 SES surface, shown, 192836 triangles
#1.75, CVA6.A_particles.5XS4.cif_B_21 SES surface, shown, 191752 triangles
#1.76, CVA6.A_particles.5XS4.cif_B_22 SES surface, shown, 192810 triangles
#1.77, CVA6.A_particles.5XS4.cif_B_23 SES surface, shown, 191038 triangles
#1.78, CVA6.A_particles.5XS4.cif_B_24 SES surface, shown, 191596 triangles
#1.79, CVA6.A_particles.5XS4.cif_B_25 SES surface, shown, 192900 triangles
#1.80, CVA6.A_particles.5XS4.cif_B_26 SES surface, shown, 192794 triangles
#1.81, CVA6.A_particles.5XS4.cif_B_27 SES surface, shown, 191172 triangles
#1.82, CVA6.A_particles.5XS4.cif_B_28 SES surface, shown, 191818 triangles
#1.83, CVA6.A_particles.5XS4.cif_B_29 SES surface, shown, 192774 triangles
#1.84, CVA6.A_particles.5XS4.cif_B_3 SES surface, shown, 191976 triangles
#1.85, CVA6.A_particles.5XS4.cif_B_30 SES surface, shown, 191770 triangles
#1.86, CVA6.A_particles.5XS4.cif_B_31 SES surface, shown, 192078 triangles
#1.87, CVA6.A_particles.5XS4.cif_B_32 SES surface, shown, 192380 triangles
#1.88, CVA6.A_particles.5XS4.cif_B_33 SES surface, shown, 191408 triangles
#1.89, CVA6.A_particles.5XS4.cif_B_34 SES surface, shown, 192450 triangles
#1.90, CVA6.A_particles.5XS4.cif_B_35 SES surface, shown, 192298 triangles
#1.91, CVA6.A_particles.5XS4.cif_B_36 SES surface, shown, 192622 triangles
#1.92, CVA6.A_particles.5XS4.cif_B_37 SES surface, shown, 191384 triangles
#1.93, CVA6.A_particles.5XS4.cif_B_38 SES surface, shown, 192608 triangles
#1.94, CVA6.A_particles.5XS4.cif_B_39 SES surface, shown, 192404 triangles
#1.95, CVA6.A_particles.5XS4.cif_B_4 SES surface, shown, 192956 triangles
#1.96, CVA6.A_particles.5XS4.cif_B_40 SES surface, shown, 192068 triangles
#1.97, CVA6.A_particles.5XS4.cif_B_41 SES surface, shown, 191564 triangles
#1.98, CVA6.A_particles.5XS4.cif_B_42 SES surface, shown, 192724 triangles
#1.99, CVA6.A_particles.5XS4.cif_B_43 SES surface, shown, 191674 triangles
#1.100, CVA6.A_particles.5XS4.cif_B_44 SES surface, shown, 192670 triangles
#1.101, CVA6.A_particles.5XS4.cif_B_45 SES surface, shown, 191118 triangles
#1.102, CVA6.A_particles.5XS4.cif_B_46 SES surface, shown, 192008 triangles
#1.103, CVA6.A_particles.5XS4.cif_B_47 SES surface, shown, 191984 triangles
#1.104, CVA6.A_particles.5XS4.cif_B_48 SES surface, shown, 191194 triangles
#1.105, CVA6.A_particles.5XS4.cif_B_49 SES surface, shown, 192882 triangles
#1.106, CVA6.A_particles.5XS4.cif_B_5 SES surface, shown, 190590 triangles
#1.107, CVA6.A_particles.5XS4.cif_B_50 SES surface, shown, 192116 triangles
#1.108, CVA6.A_particles.5XS4.cif_B_51 SES surface, shown, 190718 triangles
#1.109, CVA6.A_particles.5XS4.cif_B_52 SES surface, shown, 191014 triangles
#1.110, CVA6.A_particles.5XS4.cif_B_53 SES surface, shown, 191410 triangles
#1.111, CVA6.A_particles.5XS4.cif_B_54 SES surface, shown, 192024 triangles
#1.112, CVA6.A_particles.5XS4.cif_B_55 SES surface, shown, 192922 triangles
#1.113, CVA6.A_particles.5XS4.cif_B_56 SES surface, shown, 192246 triangles
#1.114, CVA6.A_particles.5XS4.cif_B_57 SES surface, shown, 192198 triangles
#1.115, CVA6.A_particles.5XS4.cif_B_58 SES surface, shown, 192108 triangles
#1.116, CVA6.A_particles.5XS4.cif_B_59 SES surface, shown, 192462 triangles
#1.117, CVA6.A_particles.5XS4.cif_B_6 SES surface, shown, 192146 triangles
#1.118, CVA6.A_particles.5XS4.cif_B_60 SES surface, shown, 191374 triangles
#1.119, CVA6.A_particles.5XS4.cif_B_7 SES surface, shown, 191316 triangles
#1.120, CVA6.A_particles.5XS4.cif_B_8 SES surface, shown, 192918 triangles
#1.121, CVA6.A_particles.5XS4.cif_B_9 SES surface, shown, 192288 triangles
#1.122, CVA6.A_particles.5XS4.cif_C SES surface, shown, 217544 triangles
#1.123, CVA6.A_particles.5XS4.cif_C_10 SES surface, shown, 219240 triangles
#1.124, CVA6.A_particles.5XS4.cif_C_11 SES surface, shown, 218744 triangles
#1.125, CVA6.A_particles.5XS4.cif_C_12 SES surface, shown, 218660 triangles
#1.126, CVA6.A_particles.5XS4.cif_C_13 SES surface, shown, 217572 triangles
#1.127, CVA6.A_particles.5XS4.cif_C_14 SES surface, shown, 218410 triangles
#1.128, CVA6.A_particles.5XS4.cif_C_15 SES surface, shown, 218742 triangles
#1.129, CVA6.A_particles.5XS4.cif_C_16 SES surface, shown, 219558 triangles
#1.130, CVA6.A_particles.5XS4.cif_C_17 SES surface, shown, 219294 triangles
#1.131, CVA6.A_particles.5XS4.cif_C_18 SES surface, shown, 219090 triangles
#1.132, CVA6.A_particles.5XS4.cif_C_19 SES surface, shown, 218176 triangles
#1.133, CVA6.A_particles.5XS4.cif_C_2 SES surface, shown, 218294 triangles
#1.134, CVA6.A_particles.5XS4.cif_C_20 SES surface, shown, 217832 triangles
#1.135, CVA6.A_particles.5XS4.cif_C_21 SES surface, shown, 218274 triangles
#1.136, CVA6.A_particles.5XS4.cif_C_22 SES surface, shown, 217126 triangles
#1.137, CVA6.A_particles.5XS4.cif_C_23 SES surface, shown, 219208 triangles
#1.138, CVA6.A_particles.5XS4.cif_C_24 SES surface, shown, 218456 triangles
#1.139, CVA6.A_particles.5XS4.cif_C_25 SES surface, shown, 219932 triangles
#1.140, CVA6.A_particles.5XS4.cif_C_26 SES surface, shown, 217372 triangles
#1.141, CVA6.A_particles.5XS4.cif_C_27 SES surface, shown, 219194 triangles
#1.142, CVA6.A_particles.5XS4.cif_C_28 SES surface, shown, 218444 triangles
#1.143, CVA6.A_particles.5XS4.cif_C_29 SES surface, shown, 219696 triangles
#1.144, CVA6.A_particles.5XS4.cif_C_3 SES surface, shown, 218810 triangles
#1.145, CVA6.A_particles.5XS4.cif_C_30 SES surface, shown, 217912 triangles
#1.146, CVA6.A_particles.5XS4.cif_C_31 SES surface, shown, 219702 triangles
#1.147, CVA6.A_particles.5XS4.cif_C_32 SES surface, shown, 219214 triangles
#1.148, CVA6.A_particles.5XS4.cif_C_33 SES surface, shown, 218068 triangles
#1.149, CVA6.A_particles.5XS4.cif_C_34 SES surface, shown, 218832 triangles
#1.150, CVA6.A_particles.5XS4.cif_C_35 SES surface, shown, 218576 triangles
#1.151, CVA6.A_particles.5XS4.cif_C_36 SES surface, shown, 219242 triangles
#1.152, CVA6.A_particles.5XS4.cif_C_37 SES surface, shown, 217850 triangles
#1.153, CVA6.A_particles.5XS4.cif_C_38 SES surface, shown, 218932 triangles
#1.154, CVA6.A_particles.5XS4.cif_C_39 SES surface, shown, 218560 triangles
#1.155, CVA6.A_particles.5XS4.cif_C_4 SES surface, shown, 218918 triangles
#1.156, CVA6.A_particles.5XS4.cif_C_40 SES surface, shown, 219598 triangles
#1.157, CVA6.A_particles.5XS4.cif_C_41 SES surface, shown, 218494 triangles
#1.158, CVA6.A_particles.5XS4.cif_C_42 SES surface, shown, 219862 triangles
#1.159, CVA6.A_particles.5XS4.cif_C_43 SES surface, shown, 218002 triangles
#1.160, CVA6.A_particles.5XS4.cif_C_44 SES surface, shown, 217426 triangles
#1.161, CVA6.A_particles.5XS4.cif_C_45 SES surface, shown, 219174 triangles
#1.162, CVA6.A_particles.5XS4.cif_C_46 SES surface, shown, 219318 triangles
#1.163, CVA6.A_particles.5XS4.cif_C_47 SES surface, shown, 218930 triangles
#1.164, CVA6.A_particles.5XS4.cif_C_48 SES surface, shown, 218438 triangles
#1.165, CVA6.A_particles.5XS4.cif_C_49 SES surface, shown, 218032 triangles
#1.166, CVA6.A_particles.5XS4.cif_C_5 SES surface, shown, 218816 triangles
#1.167, CVA6.A_particles.5XS4.cif_C_50 SES surface, shown, 219516 triangles
#1.168, CVA6.A_particles.5XS4.cif_C_51 SES surface, shown, 218712 triangles
#1.169, CVA6.A_particles.5XS4.cif_C_52 SES surface, shown, 217518 triangles
#1.170, CVA6.A_particles.5XS4.cif_C_53 SES surface, shown, 218356 triangles
#1.171, CVA6.A_particles.5XS4.cif_C_54 SES surface, shown, 218722 triangles
#1.172, CVA6.A_particles.5XS4.cif_C_55 SES surface, shown, 218864 triangles
#1.173, CVA6.A_particles.5XS4.cif_C_56 SES surface, shown, 218834 triangles
#1.174, CVA6.A_particles.5XS4.cif_C_57 SES surface, shown, 218498 triangles
#1.175, CVA6.A_particles.5XS4.cif_C_58 SES surface, shown, 219748 triangles
#1.176, CVA6.A_particles.5XS4.cif_C_59 SES surface, shown, 219226 triangles
#1.177, CVA6.A_particles.5XS4.cif_C_6 SES surface, shown, 218966 triangles
#1.178, CVA6.A_particles.5XS4.cif_C_60 SES surface, shown, 217990 triangles
#1.179, CVA6.A_particles.5XS4.cif_C_7 SES surface, shown, 218442 triangles
#1.180, CVA6.A_particles.5XS4.cif_C_8 SES surface, shown, 217840 triangles
#1.181, CVA6.A_particles.5XS4.cif_C_9 SES surface, shown, 219536 triangles
> save /home/dell/Desktop/2510-SongPu/CVA6.pdb models #1 relModel #4
Chain IDs longer than 2 characters; truncating
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> save /home/dell/Desktop/2510-SongPu/CVA6.cif models #1 relModel #4
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/mmcif/__init__.py", line 112, in save
mmcif_write.write_mmcif(session, path, **kw)
File "src/mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src/mmcif_write.pyx", line 156, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src/mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src/mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src/mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
ValueError: not a legal chain id
ValueError: not a legal chain id
File "src/mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
See log for complete Python traceback.
> save /home/dell/Desktop/2510-SongPu/CVA6.cif models #1 relModel #4
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/mmcif/__init__.py", line 112, in save
mmcif_write.write_mmcif(session, path, **kw)
File "src/mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src/mmcif_write.pyx", line 156, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src/mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src/mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src/mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
ValueError: not a legal chain id
ValueError: not a legal chain id
File "src/mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 530.30.02
OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900K
Cache Size: 36864 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 17Gi 72Gi 551Mi 35Gi 107Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2684] (rev a1)
Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:5108]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46
ChimeraX-AtomicLibrary: 10.0.7
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: 2.10.3
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202306232350
ChimeraX-CoreFormats: 1.1
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: 1.1.2
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: 1.2.1
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: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
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: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
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: 2.2.1
ChimeraX-TapeMeasure: 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: 1.30
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.40.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2023.3.16
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.8.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.6
PyOpenGL-accelerate: 3.1.6
pyparsing: 3.1.0
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.8.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.6.3
tzdata: 2023.3
urllib3: 2.0.3
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
Change History (1)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Save mmCIF: not a legal chain id (underscore) |
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Version 1.7, so possibly currently moot