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Opened 3 years ago
Last modified 3 years ago
#8755 assigned defect
"select clear" during simulation: Called setParameter() with invalid parameter name
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open emd-27982
'emd-27982' has no suffix
> open emd27982
'emd27982' has no suffix
> open emd 27982
'emd' has no suffix
> open 27982
'27982' has no suffix
> open emdb:27982
Summary of feedback from opening 27982 fetched from emdb
---
note | Fetching compressed map 27982 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-27982/map/emd_27982.map.gz
Opened emdb 27982 as #1, grid size 336,336,336, pixel 1.07, shown at level
0.0142, step 2, values float32
> open pdb:8eaq
Summary of feedback from opening 8eaq fetched from pdb
---
notes | Fetching compressed mmCIF 8eaq from
http://files.rcsb.org/download/8eaq.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif
Fetching CCD PLX from http://ligand-expo.rcsb.org/reports/P/PLX/PLX.cif
8eaq title:
Structure of the full-length IP3R1 channel determined at high Ca2+ [more
info...]
Chain information for 8eaq #2
---
Chain | Description | UniProt
A B C D | Inositol 1,4,5-trisphosphate receptor type 1 | ITPR1_RAT
Non-standard residues in 8eaq #2
---
CA — calcium ion
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol
ZN — zinc ion
> open emdb:27983
Summary of feedback from opening 27983 fetched from emdb
---
note | Fetching compressed map 27983 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-27983/map/emd_27983.map.gz
Opened emdb 27983 as #3, grid size 336,336,336, pixel 1.07, shown at level
0.013, step 2, values float32
> open 8ear
Summary of feedback from opening 8ear fetched from pdb
---
notes | Fetching compressed mmCIF 8ear from
http://files.rcsb.org/download/8ear.cif
Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif
Fetching CCD I3P from http://ligand-expo.rcsb.org/reports/I/I3P/I3P.cif
8ear title:
Structure of the full-length IP3R1 channel determined in the presence of
Calcium/IP3/ATP [more info...]
Chain information for 8ear #4
---
Chain | Description | UniProt
A B C D | Inositol 1,4,5-trisphosphate receptor type 1 | ITPR1_RAT
Non-standard residues in 8ear #4
---
ATP — adenosine-5'-triphosphate
CA — calcium ion
I3P — D-myo-inositol-1,4,5-triphosphate
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol
ZN — zinc ion
> volume #1 step 1
> volume #3 step 1
> hide #!4 models
> hide #!3 models
> set bgColor white
> lighting soft
> lighting simple
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!2 atoms
> hide #!2 atoms
> hide #!2 cartoons
[Repeated 2 time(s)]
> show #!2 atoms
[Repeated 1 time(s)]
> hide #!2 atoms
> show #!2 cartoons
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!2 atoms
> view :2808
> show #!3 models
> show #!4 models
> view :2808 orient
> view :5104 orient
> view :5104 center
Expected an integer >= 1 or a keyword
> view center :5104
Expected an objects specifier or a view name or a keyword
> view orient :5104
Expected a keyword
> view :5104
> view :5104 center
Expected an integer >= 1 or a keyword
> view :5104 orient
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> lighting soft
> hide #!2 cartoons
> view :5104
> view :300
> view /A:300
> view /A:5104
> hide #!2 cartoons
[Repeated 1 time(s)]
> hide #!2 atoms
> show #!2 cartoons
> style #!2 ball
Changed 77884 atom styles
> show #!2 atoms
> volume #1 color #76d6ff
> volume #1 color #76d6ff80
> volume all sdLevel 6
> volume all sdLevel 4
> volume all sdLevel 10
> volume all sdLevel 6
> volume all rmsLevel 6
> volume all sdLevel 2
> volume all sdLevel 3
> volume all sdLevel 4
> volume all sdLevel 5
> volume all sdLevel 4
> distance /A:5104 radius 3
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable object and one or more atoms, got 1 atoms and 0
measurable objects
> distance /A:5104 /A radius 3
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable object and one or more atoms, got 39084 atoms and 0
measurable objects
> distance /A:5104 /A:2583 radius 3
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable object and one or more atoms, got 17 atoms and 0
measurable objects
> distance /A:5104 /A:2583
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable object and one or more atoms, got 17 atoms and 0
measurable objects
> volume voxelLimitForOpen 4096
> volume showPlane false
> volume voxelLimitForPlane 4096
> volume dataCacheSize 4096
> camera ortho
> windowsize 900 900
> hide #!2 models
> show #!3 models
> show #!4 models
> hide #!4 cartoons
> hide #!4 atoms
> style #!4 ball
Changed 78448 atom styles
> hide #!4 cartoons
> show #!4 cartoons
> volume #3 color #73fa79
> volume #3 color #73fa7980
> show #!4 atoms
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> view #2/A:5104
> ui tool show "Side View"
> style #!2 stick
Changed 77884 atom styles
> color byelement
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> color #2 #73fdffff
> color #4 #73fa79ff
> color byelement
> show #!1 models
> save /Users/navid/Desktop/8EAQ-Ca1-5104.png format png transparentBackground
> true
> view #2/A:5106
> volume #1 level 0.01244
> save /Users/navid/Desktop/8EAQ-Ca2-5106.png format png transparentBackground
> true
> volume all sdLevel 5
> save /Users/navid/Desktop/8EAQ-Ca2-5106.png format png transparentBackground
> true
> view #2/A:5105
> view #2/A:5106 center
Expected an integer >= 1 or a keyword
> view #2/A:5106 orient
> view #2/A:5105 orient
[Repeated 1 time(s)]
> save /Users/navid/Desktop/8EAQ-Ca3-5105.png format png transparentBackground
> true
> view #2/A:5103 orient
> save /Users/navid/Desktop/8EAQ-Ca4-5103.png format png transparentBackground
> true
> view #2/A:5102 orient
[Repeated 1 time(s)]
> view #2/A:5103 orient
> view #2/A:5102 orient
> save /Users/navid/Desktop/8EAQ-Ca5-5102.png format png transparentBackground
> true
> lighting soft
[Repeated 3 time(s)]
> lighting simple
> lighting soft
> view #2/A:5106 orient
> save /Users/navid/Desktop/Serysheva.cxs
> close all
> open /Users/navid/Downloads/cryosparc_P45_J986_003_volume_map_sharp.mrc
> /Users/navid/Downloads/cryosparc_P45_J981_004_volume_map_sharp.mrc
> /Users/navid/Downloads/cryosparc_P45_J2530_004_volume_map_sharp.mrc
Opened cryosparc_P45_J986_003_volume_map_sharp.mrc as #1.1, grid size
512,512,512, pixel 0.826, shown at level 0.171, step 2, values float32
Opened cryosparc_P45_J981_004_volume_map_sharp.mrc as #1.2, grid size
512,512,512, pixel 0.826, shown at level 0.17, step 2, values float32
Opened cryosparc_P45_J2530_004_volume_map_sharp.mrc as #1.3, grid size
512,512,512, pixel 0.826, shown at level 0.182, step 2, values float32
> turn x 90
[Repeated 1 time(s)]
> open 6dqs
Summary of feedback from opening 6dqs fetched from pdb
---
warnings | Atom H is not in the residue template for PRO /A:1436
Atom H is not in the residue template for PRO /A:1494
Atom H is not in the residue template for PRO /A:1543
Atom H is not in the residue template for PRO /A:1547
Atom H is not in the residue template for PRO /B:1436
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
note | Fetching compressed mmCIF 6dqs from
http://files.rcsb.org/download/6dqs.cif
6dqs title:
Class 3 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor [more
info...]
Chain information for 6dqs #2
---
Chain | Description | UniProt
A B C D | Inositol 1,4,5-trisphosphate receptor type 3 | ITPR3_HUMAN
Non-standard residues in 6dqs #2
---
I3P — D-myo-inositol-1,4,5-triphosphate
ZN — zinc ion
> open 6dqz
Summary of feedback from opening 6dqz fetched from pdb
---
warnings | Atom H is not in the residue template for PRO /A:1501
Atom H is not in the residue template for PRO /A:1543
Atom H is not in the residue template for PRO /A:1547
Atom H is not in the residue template for PRO /B:1501
Atom H is not in the residue template for PRO /B:1543
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
note | Fetching compressed mmCIF 6dqz from
http://files.rcsb.org/download/6dqz.cif
6dqz title:
Class 4 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor [more
info...]
Chain information for 6dqz #3
---
Chain | Description | UniProt
A B C D | Inositol 1,4,5-trisphosphate receptor type 3 | ITPR3_HUMAN
Non-standard residues in 6dqz #3
---
I3P — D-myo-inositol-1,4,5-triphosphate
ZN — zinc ion
> open 6dr0
Summary of feedback from opening 6dr0 fetched from pdb
---
warnings | Atom H is not in the residue template for PRO /A:1501
Atom H is not in the residue template for PRO /A:1543
Atom H is not in the residue template for PRO /A:1547
Atom H is not in the residue template for PRO /B:1501
Atom H is not in the residue template for PRO /B:1543
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
note | Fetching compressed mmCIF 6dr0 from
http://files.rcsb.org/download/6dr0.cif
6dr0 title:
Class 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor [more
info...]
Chain information for 6dr0 #4
---
Chain | Description | UniProt
A B C D | Inositol 1,4,5-trisphosphate receptor type 3 | ITPR3_HUMAN
Non-standard residues in 6dr0 #4
---
I3P — D-myo-inositol-1,4,5-triphosphate
ZN — zinc ion
> hide #!3 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> fitmap #4 inMap #1.1
Fit molecule 6dr0 (#4) to map cryosparc_P45_J986_003_volume_map_sharp.mrc
(#1.1) using 140024 atoms
average map value = 0.1933, steps = 112
shifted from previous position = 5.8
rotated from previous position = 1.46 degrees
atoms outside contour = 65981, contour level = 0.17097
Position of 6dr0 (#4) relative to cryosparc_P45_J986_003_volume_map_sharp.mrc
(#1.1) coordinates:
Matrix rotation and translation
0.99967765 0.00472671 0.02494521 -3.35600928
-0.00465997 0.99998541 -0.00273287 4.25992769
-0.02495777 0.00261575 0.99968508 9.16843441
Axis 0.10475357 0.97735849 -0.18383978
Axis point 381.14873360 0.00000000 148.39008921
Rotation angle (degrees) 1.46289245
Shift along axis 2.12639959
> turn #4 z 90
Expected an axis vector or a keyword
> turn z 90 models #4
> fitmap #4 inMap #1.1
Fit molecule 6dr0 (#4) to map cryosparc_P45_J986_003_volume_map_sharp.mrc
(#1.1) using 140024 atoms
average map value = 0.1984, steps = 64
shifted from previous position = 4.94
rotated from previous position = 0.116 degrees
atoms outside contour = 63838, contour level = 0.17097
Position of 6dr0 (#4) relative to cryosparc_P45_J986_003_volume_map_sharp.mrc
(#1.1) coordinates:
Matrix rotation and translation
-0.00343209 0.99999336 -0.00122418 3.57261440
-0.99966804 -0.00346223 -0.02553085 426.13016803
-0.02553492 0.00113615 0.99967329 9.65730103
Axis 0.01333359 0.01215545 -0.99983722
Axis point 214.20927913 211.31420800 0.00000000
Rotation angle (degrees) 90.20686776
Shift along axis -4.42829065
> turn z 90 models #4
> fitmap #4 inMap #1.1
Fit molecule 6dr0 (#4) to map cryosparc_P45_J986_003_volume_map_sharp.mrc
(#1.1) using 140024 atoms
average map value = 0.2019, steps = 72
shifted from previous position = 4.89
rotated from previous position = 0.0636 degrees
atoms outside contour = 62463, contour level = 0.17097
Position of 6dr0 (#4) relative to cryosparc_P45_J986_003_volume_map_sharp.mrc
(#1.1) coordinates:
Matrix rotation and translation
-0.99965878 -0.00285040 -0.02596543 426.10160832
0.00279872 -0.99999403 0.00202654 419.29377224
-0.02597106 0.00195318 0.99966079 9.54342165
Axis -0.01298525 0.00099501 0.99991519
Axis point 212.81664314 209.94311775 0.00000000
Rotation angle (degrees) 179.83815052
Shift along axis 4.42678003
> turn z 90 models #4
> fitmap #4 inMap #1.1
Fit molecule 6dr0 (#4) to map cryosparc_P45_J986_003_volume_map_sharp.mrc
(#1.1) using 140024 atoms
average map value = 0.2072, steps = 72
shifted from previous position = 4.85
rotated from previous position = 0.043 degrees
atoms outside contour = 59708, contour level = 0.17097
Position of 6dr0 (#4) relative to cryosparc_P45_J986_003_volume_map_sharp.mrc
(#1.1) coordinates:
Matrix rotation and translation
0.00218321 -0.99999632 0.00160745 419.51137638
0.99966286 0.00222407 0.02586944 -3.01503533
-0.02587292 0.00155043 0.99966404 9.63346307
Axis -0.01215953 0.01374022 0.99983166
Axis point 211.35602155 208.67214482 0.00000000
Rotation angle (degrees) 89.88336535
Shift along axis 4.48935222
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!1.2 models
> hide #!1.1 models
> fitmap #3 inMap #1.2
Fit molecule 6dqz (#3) to map cryosparc_P45_J981_004_volume_map_sharp.mrc
(#1.2) using 139662 atoms
average map value = 0.1957, steps = 72
shifted from previous position = 5.95
rotated from previous position = 0.758 degrees
atoms outside contour = 63858, contour level = 0.16984
Position of 6dqz (#3) relative to cryosparc_P45_J981_004_volume_map_sharp.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.99991947 0.00027907 -0.01268753 5.21291123
-0.00032621 0.99999305 -0.00371311 3.45657685
0.01268641 0.00371695 0.99991262 1.15118053
Axis 0.28094849 -0.95944991 -0.02288713
Axis point -84.23263563 0.00000000 452.99371829
Rotation angle (degrees) 0.75765389
Shift along axis -1.87820000
> hide #!3 models
> show #!3 models
> turn z 90 models #3
> fitmap #3 inMap #1.2
Fit molecule 6dqz (#3) to map cryosparc_P45_J981_004_volume_map_sharp.mrc
(#1.2) using 139662 atoms
average map value = 0.1802, steps = 68
shifted from previous position = 4.76
rotated from previous position = 0.218 degrees
atoms outside contour = 70663, contour level = 0.16984
Position of 6dqz (#3) relative to cryosparc_P45_J981_004_volume_map_sharp.mrc
(#1.2) coordinates:
Matrix rotation and translation
0.00289441 0.99998453 -0.00474896 3.06916799
-0.99989188 0.00296255 0.01440298 416.76130896
0.01441683 0.00470676 0.99988499 0.63978566
Axis -0.00484813 -0.00958294 -0.99994233
Axis point 210.50251952 206.84980507 0.00000000
Rotation angle (degrees) 89.83550486
Shift along axis -4.64842512
> turn z 90 models #3
> fitmap #3 inMap #1.2
Fit molecule 6dqz (#3) to map cryosparc_P45_J981_004_volume_map_sharp.mrc
(#1.2) using 139662 atoms
average map value = 0.1901, steps = 76
shifted from previous position = 4.89
rotated from previous position = 0.148 degrees
atoms outside contour = 66160, contour level = 0.16984
Position of 6dqz (#3) relative to cryosparc_P45_J981_004_volume_map_sharp.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.99988035 0.00554336 0.01444150 416.16736250
-0.00547595 -0.99997395 0.00470310 420.40665170
0.01446719 0.00462346 0.99988466 0.64259717
Axis -0.00722743 -0.00233173 -0.99997116
Axis point 208.66045583 209.62935070 0.00000000
Rotation angle (degrees) 179.68430932
Shift along axis -4.63067425
> turn z 90 models #3
> fitmap #3 inMap #1.2
Fit molecule 6dqz (#3) to map cryosparc_P45_J981_004_volume_map_sharp.mrc
(#1.2) using 139662 atoms
average map value = 0.207, steps = 68
shifted from previous position = 4.84
rotated from previous position = 0.233 degrees
atoms outside contour = 58635, contour level = 0.16984
Position of 6dqz (#3) relative to cryosparc_P45_J981_004_volume_map_sharp.mrc
(#1.2) coordinates:
Matrix rotation and translation
-0.00181802 -0.99998768 0.00461963 419.70402222
0.99991803 -0.00187641 -0.01266525 5.62921416
0.01267376 0.00459622 0.99990912 0.96433169
Axis 0.00863075 -0.00402707 0.99995465
Axis point 207.02926423 212.26159934 0.00000000
Rotation angle (degrees) 90.10844110
Shift along axis 4.56397959
> show #!2 models
> hide #!3 models
> show #!1.3 models
> hide #!1.2 models
> fitmap #2 inMap #1.3
Fit molecule 6dqs (#2) to map cryosparc_P45_J2530_004_volume_map_sharp.mrc
(#1.3) using 139350 atoms
average map value = 0.2937, steps = 84
shifted from previous position = 5.69
rotated from previous position = 2.43 degrees
atoms outside contour = 56299, contour level = 0.1822
Position of 6dqs (#2) relative to cryosparc_P45_J2530_004_volume_map_sharp.mrc
(#1.3) coordinates:
Matrix rotation and translation
0.99957149 0.00890259 -0.02788529 5.65796700
-0.00804147 0.99949192 0.03084197 -1.74221082
0.02814570 -0.03060452 0.99913522 5.35800521
Axis -0.72404100 -0.66022867 -0.19965654
Axis point 0.00000000 144.77940778 144.84533758
Rotation angle (degrees) 2.43196322
Shift along axis -4.01610331
> turn z 90 models #2
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #1.3
Fit molecule 6dqs (#2) to map cryosparc_P45_J2530_004_volume_map_sharp.mrc
(#1.3) using 139350 atoms
average map value = 0.2621, steps = 72
shifted from previous position = 4.92
rotated from previous position = 0.15 degrees
atoms outside contour = 64251, contour level = 0.1822
Position of 6dqs (#2) relative to cryosparc_P45_J2530_004_volume_map_sharp.mrc
(#1.3) coordinates:
Matrix rotation and translation
-0.00909073 0.99951311 0.02984795 -1.15845023
-0.99949926 -0.00998722 0.03002485 416.89678367
0.03030833 -0.02956006 0.99910340 4.59872099
Axis -0.02979394 -0.00023020 -0.99955604
Axis point 205.82022509 209.09031882 0.00000000
Rotation angle (degrees) 90.57223801
Shift along axis -4.65813363
> turn z 90 models #2
> fitmap #2 inMap #1.3
Fit molecule 6dqs (#2) to map cryosparc_P45_J2530_004_volume_map_sharp.mrc
(#1.3) using 139350 atoms
average map value = 0.2716, steps = 76
shifted from previous position = 4.8
rotated from previous position = 0.436 degrees
atoms outside contour = 61688, contour level = 0.1822
Position of 6dqs (#2) relative to cryosparc_P45_J2530_004_volume_map_sharp.mrc
(#1.3) coordinates:
Matrix rotation and translation
-0.99949124 -0.01650885 0.02728965 419.10938653
0.01576597 -0.99950522 -0.02721672 422.05825008
0.02772546 -0.02677262 0.99925699 4.53772359
Axis 0.01375723 -0.01350072 0.99981422
Axis point 207.81974809 212.75107961 0.00000000
Rotation angle (degrees) 179.07518273
Shift along axis 4.60457340
> turn z 90 models #2
> fitmap #2 inMap #1.3
Fit molecule 6dqs (#2) to map cryosparc_P45_J2530_004_volume_map_sharp.mrc
(#1.3) using 139350 atoms
average map value = 0.3081, steps = 84
shifted from previous position = 4.79
rotated from previous position = 0.264 degrees
atoms outside contour = 51209, contour level = 0.1822
Position of 6dqs (#2) relative to cryosparc_P45_J2530_004_volume_map_sharp.mrc
(#1.3) coordinates:
Matrix rotation and translation
0.01210256 -0.99950059 -0.02919083 423.49102919
0.99959440 0.01284600 -0.02541693 4.12713396
0.02577922 -0.02887138 0.99925066 5.46392680
Axis -0.00172735 -0.02748704 0.99962067
Axis point 209.59650542 216.54729867 0.00000000
Rotation angle (degrees) 89.30672661
Shift along axis 4.61689341
> hide #!2 models
> show #!2 models
> open "/Users/navid/Library/CloudStorage/GoogleDrive-nav2686@gmail.com/My
> Drive/Science/Projects/hIP3R3_Titration/Maps/J1311-DM.ccp4"
> "/Users/navid/Library/CloudStorage/GoogleDrive-nav2686@gmail.com/My
> Drive/Science/Projects/hIP3R3_Titration/Maps/J986-DM.ccp4"
> "/Users/navid/Library/CloudStorage/GoogleDrive-nav2686@gmail.com/My
> Drive/Science/Projects/hIP3R3_Titration/Maps/J981-DM.ccp4"
Opened J1311-DM.ccp4 as #5.1, grid size 512,512,512, pixel 0.826, shown at
level 0.869, step 2, values float32
Opened J986-DM.ccp4 as #5.2, grid size 512,512,512, pixel 0.826, shown at
level 0.857, step 2, values float32
Opened J981-DM.ccp4 as #5.3, grid size 512,512,512, pixel 0.826, shown at
level 0.878, step 2, values float32
> volume #0-100 step 1
> volume voxelLimitForOpen 8192
> volume showPlane false
> volume voxelLimitForPlane 8192
> volume dataCacheSize 8192
> close #5
> open "/Users/navid/Library/CloudStorage/GoogleDrive-nav2686@gmail.com/My
> Drive/Science/Projects/hIP3R3_Titration/Maps/J1311-DM.ccp4"
> "/Users/navid/Library/CloudStorage/GoogleDrive-nav2686@gmail.com/My
> Drive/Science/Projects/hIP3R3_Titration/Maps/J986-DM.ccp4"
> "/Users/navid/Library/CloudStorage/GoogleDrive-nav2686@gmail.com/My
> Drive/Science/Projects/hIP3R3_Titration/Maps/J981-DM.ccp4"
Opened J1311-DM.ccp4 as #5.1, grid size 512,512,512, pixel 0.826, shown at
level 0.869, step 2, values float32
Opened J986-DM.ccp4 as #5.2, grid size 512,512,512, pixel 0.826, shown at
level 0.857, step 2, values float32
Opened J981-DM.ccp4 as #5.3, grid size 512,512,512, pixel 0.826, shown at
level 0.878, step 2, values float32
> volume #0-100 step 1
> volume #0-100 fastEncloseVolume 1500000
> volume #0-100 fastEncloseVolume 750000
> volume #0-100 fastEncloseVolume 500000
> set bgColor white
> lighting soft
> close #1.1
> close #1.2
> close #1.3
> volume #0-100 fastEncloseVolume 250000
> hide #!2 models
> name BTF1 :1-228
> name BTF2 :229-434
> name ARM1 :435-664
> name CLD :665-1100,1570-1640,1676-1697
> name ARM2 :1101-1569
> name ARM3 :1641-1675,1698-2092
> name JD :2093-2191,2538-2611
> name TMD :2192-2537
> name CTD :2612-2671
> name IP3 :3002
> name ATP :3005
> name Zn2+ :3001
> name JD-Ca2+ :3003
> name CD-Ca2+ :3004
> name Mg2+ :3006
> color BTF1 #8033ff
> color BTF2 #4040ff
> color ARM1 #bfbfff
> color CLD #33ffff
> color ARM2 #33ff33
> color ARM3 #ffff33
> color JD #ff8c26
> color TMD #ff3333
> color CTD #991a99
> color IP3 yellow
> color ATP blue
> color Zn2+ blue
> color JD-Ca2+ green
> color CD-Ca2+ magenta
> color Mg2+ yellow
> color solvent aquamarine
> graphics silhouettes depthJump 0.05
> graphics silhouettes width 1
> lighting multiShadow 512
> camera ortho
> windowsize 900 900
> hide #!5.1 models
> hide #!5.2 models
> hide #!5.3 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!5.3 models
> show #!5.2 models
> show #!5.1 models
> hide #!5.2 models
> hide #!5.1 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5.3 models
> show #!5.3 models
> fitmap #2 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 139350 atoms
average map value = 0.975, steps = 96
shifted from previous position = 0.121
rotated from previous position = 1.63 degrees
atoms outside contour = 111287, contour level = 2.6204
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.04061127 -0.99874029 -0.02947144 417.36158473
0.99883789 0.04134606 -0.02476631 -1.78132869
0.02595364 -0.02843140 0.99925876 5.44832230
Axis -0.00183405 -0.02773542 0.99961362
Axis point 209.54540373 216.60762520 0.00000000
Rotation angle (degrees) 87.67269054
Shift along axis 4.73015945
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false color zone #5.3 near #2
> distance 2.5
Expected a keyword
> hide #!2 models
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false color zone #5.3 near #2
> distance 2.5
Expected a keyword
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false
> color zone #5.3 near #2 distance 2.5
> volume zone #5.2 nearAtoms #3 range 2.5 newMap false
> color zone #5.2 near #3 distance 2.5
> fitmap #3 inMap #5.2
Fit molecule 6dqz (#3) to map J986-DM.ccp4 (#5.2) using 139662 atoms
average map value = 1.436, steps = 44
shifted from previous position = 0.116
rotated from previous position = 0.0682 degrees
atoms outside contour = 105069, contour level = 2.5568
Position of 6dqz (#3) relative to J986-DM.ccp4 (#5.2) coordinates:
Matrix rotation and translation
-0.00115912 -0.99998619 0.00512533 419.37842128
0.99990784 -0.00122833 -0.01352041 5.64254873
0.01352651 0.00510918 0.99989546 0.75507293
Axis 0.00931480 -0.00420060 0.99994779
Axis point 206.85805635 212.24032231 0.00000000
Rotation angle (degrees) 90.07139013
Shift along axis 4.63775860
> volume zone #5.2 nearAtoms #3 range 2.5 newMap false
> color zone #5.2 near #3 distance 2.5
> fitmap #4 inMap #5.1
Fit molecule 6dr0 (#4) to map J1311-DM.ccp4 (#5.1) using 140024 atoms
average map value = 1.229, steps = 76
shifted from previous position = 0.324
rotated from previous position = 0.938 degrees
atoms outside contour = 109363, contour level = 2.786
Position of 6dr0 (#4) relative to J1311-DM.ccp4 (#5.1) coordinates:
Matrix rotation and translation
-0.01379757 -0.99990298 -0.00191465 423.80350871
0.99955150 -0.01384357 0.02655463 0.07387535
-0.02657856 -0.00154740 0.99964553 10.43584531
Axis -0.01405239 0.01233317 0.99982520
Axis point 211.96590475 208.99621379 0.00000000
Rotation angle (degrees) 90.80204151
Shift along axis 4.47947901
> volume zone #5.1 nearAtoms #4 range 2.5 newMap false
> color zone #5.1 near #4 distance 2.5
> show #!5.2 models
> show #!5.1 models
> hide #!5.1 models
> hide #!5.2 models
> hide #!5.3 models
> show #!2 models
> show #!2 cartoons
> style #!2 stick
Changed 139350 atom styles
> hide #!2 cartoons
> hide #!2 atoms
> show #!2 cartoons
> style #!2 stick
Changed 139350 atom styles
> show #!2 atoms
[Repeated 1 time(s)]
> view #2/A:3002
> view #2/A:3002 orient
> view #2/A:3002
> show #!5.1 models
> hide #!5.1 models
> show #!5.3 models
> fitmap #2/A inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 34730 atoms
average map value = 0.9302, steps = 116
shifted from previous position = 1.57
rotated from previous position = 1.72 degrees
atoms outside contour = 27752, contour level = 2.6204
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.01592332 -0.99945210 -0.02901621 422.20461936
0.99894336 0.01715306 -0.04263717 8.16297319
0.04311153 -0.02830663 0.99866918 1.79398307
Axis 0.00716618 -0.03606841 0.99932363
Axis point 206.86332997 218.72265799 0.00000000
Rotation angle (degrees) 89.09051856
Shift along axis 4.52393673
> fitmap #2/A:1-600 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 8916 atoms
average map value = 1.848, steps = 76
shifted from previous position = 1.96
rotated from previous position = 3.22 degrees
atoms outside contour = 6124, contour level = 2.6204
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.05687148 -0.99613889 -0.06688014 419.16134560
0.99711645 0.06004304 -0.04640711 -1.31819482
0.05024361 -0.06404805 0.99668121 11.52990273
Axis -0.00883473 -0.05865657 0.99823913
Axis point 210.08540796 221.95043270 0.00000000
Rotation angle (degrees) 86.74396991
Shift along axis 7.88374366
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false
> color zone #5.3 near #2 distance 2.5
> view #2/A:3002
> view #2/A:3002 orient
> color #5.3 #b2ffb280 models
> color #5.3 #b2ffb2ff models
> color #5.3 #b2ffb280 models
> color zone #5.3 near #2 distance 2.5
> save /Users/navid/Desktop/J981-6DQS-ChainA.png format png
> transparentBackground true
> fitmap #2/B:1-600 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 8916 atoms
average map value = 1.995, steps = 84
shifted from previous position = 0.964
rotated from previous position = 1.41 degrees
atoms outside contour = 5958, contour level = 2.6204
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.05910710 -0.99724100 -0.04490822 415.74001493
0.99647190 0.06162712 -0.05697230 -0.48325394
0.05958268 -0.04138231 0.99736523 4.25067285
Axis 0.00780862 -0.05233677 0.99859896
Axis point 207.90112757 220.67747786 0.00000000
Rotation angle (degrees) 86.61473064
Shift along axis 7.51636536
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false
> color zone #5.3 near #2 distance 2.5
> view #2/B:3002 orient
> turn x 45
> turn y 45
[Repeated 2 time(s)]
> save /Users/navid/Desktop/J981-6DQS-ChainB.png format png
> transparentBackground true
> fitmap #2/C:1-600 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 8915 atoms
average map value = 2.111, steps = 56
shifted from previous position = 1.69
rotated from previous position = 1.79 degrees
atoms outside contour = 5868, contour level = 2.6204
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.06174794 -0.99798108 -0.01486470 410.94358893
0.99685507 0.06240575 -0.04884153 -1.52902588
0.04967057 -0.01180209 0.99869592 -0.35625422
Axis 0.01855476 -0.03232868 0.99930505
Axis point 206.16278721 217.81488906 0.00000000
Rotation angle (degrees) 86.47840097
Shift along axis 7.31838392
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false
> color zone #5.3 near #2 distance 2.5
> view #2/C:3002 orient
> save /Users/navid/Desktop/J981-6DQS-ChainC.png format png
> transparentBackground true
> fitmap #2/D:1-600 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 8916 atoms
average map value = 1.985, steps = 80
shifted from previous position = 1.05
rotated from previous position = 1.4 degrees
atoms outside contour = 5911, contour level = 2.6204
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.06501843 -0.99775342 -0.01614679 409.91934758
0.99755517 0.06540389 -0.02461728 -5.79640845
0.02561804 -0.01450674 0.99956654 5.29869534
Axis 0.00506598 -0.02092666 0.99976818
Axis point 207.95635701 215.93112062 0.00000000
Rotation angle (degrees) 86.27346669
Shift along axis 7.49541167
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false
> color zone #5.3 near #2 distance 2.5
> view #2/D:3002 orient
> turn y 180
> turn z 90
[Repeated 4 time(s)]
> fitmap #2/D:1-300 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 4531 atoms
average map value = 2.771, steps = 44
shifted from previous position = 0.0981
rotated from previous position = 1.16 degrees
atoms outside contour = 2580, contour level = 2.6204
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.06731439 -0.99758444 -0.01714802 409.40152603
0.99668434 0.06802113 -0.04464801 -2.88163327
0.04570659 -0.01408571 0.99885560 0.22990358
Axis 0.01531566 -0.03149829 0.99938646
Axis point 206.12982691 217.57181829 0.00000000
Rotation angle (degrees) 86.15281729
Shift along axis 6.59078469
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false
> color zone #5.3 near #2 distance 2.5
> color zone #5.3 near #2 distance 4
> color zone #5.3 near #2 distance 2.5
> save /Users/navid/Desktop/J981-6DQS-ChainD.png format png
> transparentBackground true
> view orient
> turn x 90
[Repeated 1 time(s)]
> save /Users/navid/Desktop/J981-6DQS-OVERALL.png format png
> transparentBackground true
> volume #0-100 fastEncloseVolume 600000
> volume #0-100 fastEncloseVolume 500000
> fitmap #2/:1-300 inMap #5.3
Missing or invalid "atomsOrMap" argument: only initial part "#2" of atom
specifier valid
> fitmap #2 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 139350 atoms
average map value = 0.975, steps = 68
shifted from previous position = 1.89
rotated from previous position = 2.05 degrees
atoms outside contour = 95767, contour level = 1.3524
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.04060486 -0.99874203 -0.02942123 417.35033647
0.99883807 0.04133849 -0.02477162 -1.77864584
0.02595669 -0.02838120 0.99926011 5.43794082
Axis -0.00180628 -0.02771181 0.99961432
Axis point 209.53833285 216.60130217 0.00000000
Rotation angle (degrees) 87.67305280
Shift along axis 4.73128289
> volume zone #5.3 nearAtoms #2 range 2.5 newMap false
> volume zone #5.3 nearAtoms #2 range 5 newMap false
> color zone #5.3 near #2 distance 5
> hide #!2 atoms
> save /Users/navid/Desktop/J981-6DQS-OVERALL.png format png
> transparentBackground true
> show #!5.2 models
> hide #!5.3 models
> show #!3 models
> hide #!2 models
> style #!3 stick
Changed 139662 atom styles
> hide #!3 atoms
> show #!3 cartoons
> fitmap #3 inMap #5.2
Fit molecule 6dqz (#3) to map J986-DM.ccp4 (#5.2) using 139662 atoms
average map value = 1.436, steps = 40
shifted from previous position = 0.00931
rotated from previous position = 0.0071 degrees
atoms outside contour = 87032, contour level = 1.3246
Position of 6dqz (#3) relative to J986-DM.ccp4 (#5.2) coordinates:
Matrix rotation and translation
-0.00114950 -0.99998556 0.00524879 419.34259655
0.99990783 -0.00122038 -0.01352165 5.64274079
0.01352786 0.00523276 0.99989480 0.72872889
Axis 0.00937721 -0.00413954 0.99994746
Axis point 206.84026493 212.22414521 0.00000000
Rotation angle (degrees) 90.07090572
Shift along axis 4.63759771
> volume zone #5.2 nearAtoms #3 range 5 newMap false
> color zone #5.2 near #3 distance 5
> color zone #5.2 near #3:A/3002 distance 3
color zone: No atoms specified.
> color zone #5.2 near #3/A:3002 distance 3
> color zone #5.2 near #3 distance 5
> ui tool show ISOLDE
> set selectionWidth 4
Populating font family aliases took 166 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.
> fitmap #3 inMap #5.2
Fit molecule 6dqz (#3) to map J986-DM.ccp4 (#5.2) using 139662 atoms
average map value = 1.436, steps = 44
shifted from previous position = 0.0077
rotated from previous position = 0.00266 degrees
atoms outside contour = 87048, contour level = 1.3246
Position of 6dqz (#3) relative to J986-DM.ccp4 (#5.2) coordinates:
Matrix rotation and translation
-0.00115027 -0.99998534 0.00529145 419.32930121
0.99990808 -0.00122164 -0.01350336 5.63762875
0.01350963 0.00527543 0.99989482 0.71794605
Axis 0.00938940 -0.00410909 0.99994748
Axis point 206.83630133 212.21470135 0.00000000
Rotation angle (degrees) 90.07096332
Shift along axis 4.63199404
> clipper associate #5.2 toModel #3
Opened J986-DM.ccp4 as #3.1.1.1, grid size 512,512,512, pixel 0.826, shown at
level 3.06, step 1, values float32
6dqz title:
Class 4 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor [more
info...]
Chain information for 6dqz
---
Chain | Description | UniProt
3.2/A 3.2/B 3.2/C 3.2/D | Inositol 1,4,5-trisphosphate receptor type 3 |
ITPR3_HUMAN
Non-standard residues in 6dqz #3.2
---
I3P — D-myo-inositol-1,4,5-triphosphate
ZN — zinc ion
> set bgColor white
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to 6dqs #2/A ASP 1435 CB because it is missing
heavy-atom bond partners
Not adding hydrogens to 6dqs #2/A PRO 1436 N because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dqs #2/A PRO 1436 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dqs #2/A THR 1437 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dqs #2/A LEU 1438 CB because it is missing heavy-atom
bond partners
351 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 6dqs #2/B PRO 1436 N; 6dqs #2/A PRO 1436 N; 6dqs #2/C PRO 1436
N; 6dqs #2/C PRO 1494 N; 6dqs #2/B PRO 1494 N; 6dqs #2/C PRO 1543 N; 6dqs #2/D
PRO 1501 N; 6dqs #2/C PRO 1547 N; 6dqs #2/B PRO 1543 N; 6dqs #2/B PRO 1547 N;
6dqs #2/D PRO 1543 N; 6dqs #2/A PRO 1547 N; 6dqs #2/D PRO 1547 N; 6dqs #2/A
PRO 1543 N; 6dqs #2/A PRO 1494 N
Not adding hydrogens to 6dr0 #4/A MET 1491 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dr0 #4/A VAL 1492 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dr0 #4/A LYS 1494 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dr0 #4/A ARG 1496 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dr0 #4/A ILE 1498 CB because it is missing heavy-atom
bond partners
271 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 6dr0 #4/A PRO 1543 N; 6dr0 #4/B PRO 1543 N; 6dr0 #4/B PRO 1547
N; 6dr0 #4/C PRO 1501 N; 6dr0 #4/A PRO 1547 N; 6dr0 #4/C PRO 1543 N; 6dr0 #4/C
PRO 1547 N; 6dr0 #4/A PRO 1501 N; 6dr0 #4/D PRO 1436 N; 6dr0 #4/D PRO 1494 N;
6dr0 #4/D PRO 1543 N; 6dr0 #4/B PRO 1501 N; 6dr0 #4/D PRO 1547 N
Not adding hydrogens to 6dqz #3.2/A MET 1491 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 6dqz #3.2/A VAL 1492 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 6dqz #3.2/A LYS 1494 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 6dqz #3.2/A ARG 1496 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 6dqz #3.2/A ILE 1498 CB because it is missing heavy-
atom bond partners
311 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 6dqz #3.2/A PRO 1543 N; 6dqz #3.2/D PRO 1543 N; 6dqz #3.2/B PRO
1501 N; 6dqz #3.2/A PRO 1547 N; 6dqz #3.2/D PRO 1547 N; 6dqz #3.2/B PRO 1543
N; 6dqz #3.2/B PRO 1547 N; 6dqz #3.2/A PRO 1501 N; 6dqz #3.2/C PRO 1436 N;
6dqz #3.2/D PRO 1436 N; 6dqz #3.2/C PRO 1543 N; 6dqz #3.2/C PRO 1547 N; 6dqz
#3.2/D PRO 1494 N; 6dqz #3.2/C PRO 1494 N
notes | Termini for 6dqs (#2) chain A determined from SEQRES records
Termini for 6dqs (#2) chain B determined from SEQRES records
Termini for 6dqs (#2) chain C determined from SEQRES records
Termini for 6dqs (#2) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6dqs #2/A SER 5, 6dqs
#2/A ASP 86, 6dqs #2/A GLU 348, 6dqs #2/A GLY 533, 6dqs #2/A GLU 690, 6dqs
#2/A ASP 961, 6dqs #2/A ASN 1024, 6dqs #2/A SER 1043, 6dqs #2/A SER 1166, 6dqs
#2/A ALA 1434, 6dqs #2/A LEU 1462, 6dqs #2/A ASP 1717, 6dqs #2/A MET 1863,
6dqs #2/A GLU 2111, 6dqs #2/A LEU 2231, 6dqs #2/A ASP 2449, 6dqs #2/B SER 5,
6dqs #2/B ASP 86, 6dqs #2/B GLU 348, 6dqs #2/B GLY 533, 6dqs #2/B GLU 690,
6dqs #2/B ASP 961, 6dqs #2/B ASN 1024, 6dqs #2/B SER 1043, 6dqs #2/B SER 1166,
6dqs #2/B ALA 1434, 6dqs #2/B LEU 1462, 6dqs #2/B ASP 1717, 6dqs #2/B MET
1863, 6dqs #2/B GLU 2111, 6dqs #2/B LEU 2231, 6dqs #2/B ASP 2449, 6dqs #2/C
SER 5, 6dqs #2/C ASP 86, 6dqs #2/C GLU 348, 6dqs #2/C GLY 533, 6dqs #2/C GLU
690, 6dqs #2/C ASP 961, 6dqs #2/C ASN 1024, 6dqs #2/C SER 1043, 6dqs #2/C SER
1166, 6dqs #2/C ALA 1434, 6dqs #2/C LEU 1462, 6dqs #2/C ASP 1717, 6dqs #2/C
MET 1863, 6dqs #2/C GLU 2111, 6dqs #2/C LEU 2231, 6dqs #2/C ASP 2449, 6dqs
#2/D SER 5, 6dqs #2/D ASP 86, 6dqs #2/D GLU 348, 6dqs #2/D GLY 533, 6dqs #2/D
GLU 690, 6dqs #2/D ASP 961, 6dqs #2/D ASN 1024, 6dqs #2/D SER 1043, 6dqs #2/D
SER 1166, 6dqs #2/D THR 1463, 6dqs #2/D ALA 1490, 6dqs #2/D ALA 1515, 6dqs
#2/D TRP 1718, 6dqs #2/D MET 1863, 6dqs #2/D GLU 2111, 6dqs #2/D LEU 2231,
6dqs #2/D ASP 2449
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 6dqs #2/A THR 77, 6dqs
#2/A TYR 323, 6dqs #2/A ARG 527, 6dqs #2/A LYS 674, 6dqs #2/A ASP 893, 6dqs
#2/A PHE 1002, 6dqs #2/A VAL 1038, 6dqs #2/A VAL 1128, 6dqs #2/A ASP 1423,
6dqs #2/A PHE 1454, 6dqs #2/A GLN 1696, 6dqs #2/A VAL 1804, 6dqs #2/A VAL
2074, 6dqs #2/A TYR 2225, 6dqs #2/A PRO 2403, 6dqs #2/A VAL 2611, 6dqs #2/B
THR 77, 6dqs #2/B TYR 323, 6dqs #2/B ARG 527, 6dqs #2/B LYS 674, 6dqs #2/B ASP
893, 6dqs #2/B PHE 1002, 6dqs #2/B VAL 1038, 6dqs #2/B VAL 1128, 6dqs #2/B ASP
1423, 6dqs #2/B PHE 1454, 6dqs #2/B GLN 1696, 6dqs #2/B VAL 1804, 6dqs #2/B
VAL 2074, 6dqs #2/B TYR 2225, 6dqs #2/B PRO 2403, 6dqs #2/B VAL 2611, 6dqs
#2/C THR 77, 6dqs #2/C TYR 323, 6dqs #2/C ARG 527, 6dqs #2/C LYS 674, 6dqs
#2/C ASP 893, 6dqs #2/C PHE 1002, 6dqs #2/C VAL 1038, 6dqs #2/C VAL 1128, 6dqs
#2/C ASP 1423, 6dqs #2/C PHE 1454, 6dqs #2/C GLN 1696, 6dqs #2/C VAL 1804,
6dqs #2/C VAL 2074, 6dqs #2/C TYR 2225, 6dqs #2/C PRO 2403, 6dqs #2/C VAL
2611, 6dqs #2/D THR 77, 6dqs #2/D TYR 323, 6dqs #2/D ARG 527, 6dqs #2/D PRO
672, 6dqs #2/D ASP 893, 6dqs #2/D PHE 1002, 6dqs #2/D GLY 1037, 6dqs #2/D ASP
1129, 6dqs #2/D ARG 1455, 6dqs #2/D PRO 1483, 6dqs #2/D ILE 1508, 6dqs #2/D
GLN 1696, 6dqs #2/D VAL 1804, 6dqs #2/D VAL 2074, 6dqs #2/D TYR 2225, 6dqs
#2/D PRO 2403, 6dqs #2/D VAL 2611
5503 hydrogen bonds
Adding 'H' to 6dqs #2/A SER 5
Adding 'H' to 6dqs #2/A ASP 86
Adding 'H' to 6dqs #2/A GLU 348
Adding 'H' to 6dqs #2/A GLY 533
Adding 'H' to 6dqs #2/A GLU 690
60 messages similar to the above omitted
6dqs #2/A VAL 2611 is not terminus, removing H atom from 'C'
6dqs #2/B VAL 2611 is not terminus, removing H atom from 'C'
6dqs #2/C VAL 2611 is not terminus, removing H atom from 'C'
6dqs #2/D VAL 2611 is not terminus, removing H atom from 'C'
Termini for 6dr0 (#4) chain A determined from SEQRES records
Termini for 6dr0 (#4) chain B determined from SEQRES records
Termini for 6dr0 (#4) chain C determined from SEQRES records
Termini for 6dr0 (#4) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6dr0 #4/A SER 5, 6dr0
#4/A ASP 86, 6dr0 #4/A LYS 351, 6dr0 #4/A PRO 534, 6dr0 #4/A GLU 690, 6dr0
#4/A ASP 961, 6dr0 #4/A ASN 1024, 6dr0 #4/A SER 1043, 6dr0 #4/A SER 1166, 6dr0
#4/A THR 1463, 6dr0 #4/A ALA 1490, 6dr0 #4/A ALA 1515, 6dr0 #4/A TRP 1718,
6dr0 #4/A MET 1863, 6dr0 #4/A GLU 2111, 6dr0 #4/A LEU 2231, 6dr0 #4/A ASP
2449, 6dr0 #4/B SER 5, 6dr0 #4/B ASP 86, 6dr0 #4/B LYS 351, 6dr0 #4/B PRO 534,
6dr0 #4/B GLU 690, 6dr0 #4/B ASP 961, 6dr0 #4/B ASN 1024, 6dr0 #4/B SER 1043,
6dr0 #4/B SER 1166, 6dr0 #4/B THR 1463, 6dr0 #4/B ALA 1490, 6dr0 #4/B ALA
1515, 6dr0 #4/B TRP 1718, 6dr0 #4/B MET 1863, 6dr0 #4/B GLU 2111, 6dr0 #4/B
LEU 2231, 6dr0 #4/B ASP 2449, 6dr0 #4/C SER 5, 6dr0 #4/C ASP 86, 6dr0 #4/C GLU
348, 6dr0 #4/C GLY 533, 6dr0 #4/C GLU 690, 6dr0 #4/C ASP 961, 6dr0 #4/C ASN
1024, 6dr0 #4/C SER 1043, 6dr0 #4/C SER 1166, 6dr0 #4/C THR 1463, 6dr0 #4/C
ALA 1490, 6dr0 #4/C ALA 1515, 6dr0 #4/C TRP 1718, 6dr0 #4/C MET 1863, 6dr0
#4/C GLU 2111, 6dr0 #4/C LEU 2231, 6dr0 #4/C ASP 2449, 6dr0 #4/D SER 5, 6dr0
#4/D ASP 86, 6dr0 #4/D LYS 351, 6dr0 #4/D PRO 534, 6dr0 #4/D GLU 690, 6dr0
#4/D ASP 961, 6dr0 #4/D ASN 1024, 6dr0 #4/D SER 1043, 6dr0 #4/D SER 1166, 6dr0
#4/D ALA 1434, 6dr0 #4/D LEU 1462, 6dr0 #4/D ASP 1717, 6dr0 #4/D MET 1863,
6dr0 #4/D GLU 2111, 6dr0 #4/D LEU 2231, 6dr0 #4/D ASP 2449
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 6dr0 #4/A GLN 76, 6dr0
#4/A TYR 323, 6dr0 #4/A ARG 527, 6dr0 #4/A PRO 672, 6dr0 #4/A ASP 893, 6dr0
#4/A PRO 1003, 6dr0 #4/A GLY 1037, 6dr0 #4/A ASP 1129, 6dr0 #4/A ARG 1455,
6dr0 #4/A PRO 1483, 6dr0 #4/A ILE 1508, 6dr0 #4/A GLN 1696, 6dr0 #4/A VAL
1804, 6dr0 #4/A VAL 2074, 6dr0 #4/A TYR 2225, 6dr0 #4/A PRO 2403, 6dr0 #4/A
VAL 2611, 6dr0 #4/B GLN 76, 6dr0 #4/B TYR 323, 6dr0 #4/B ARG 527, 6dr0 #4/B
PRO 672, 6dr0 #4/B ASP 893, 6dr0 #4/B PRO 1003, 6dr0 #4/B GLY 1037, 6dr0 #4/B
ASP 1129, 6dr0 #4/B ARG 1455, 6dr0 #4/B PRO 1483, 6dr0 #4/B ILE 1508, 6dr0
#4/B GLN 1696, 6dr0 #4/B VAL 1804, 6dr0 #4/B VAL 2074, 6dr0 #4/B TYR 2225,
6dr0 #4/B PRO 2403, 6dr0 #4/B VAL 2611, 6dr0 #4/C THR 77, 6dr0 #4/C TYR 323,
6dr0 #4/C ARG 527, 6dr0 #4/C PRO 672, 6dr0 #4/C ASP 893, 6dr0 #4/C PRO 1003,
6dr0 #4/C GLY 1037, 6dr0 #4/C ASP 1129, 6dr0 #4/C ARG 1455, 6dr0 #4/C PRO
1483, 6dr0 #4/C ILE 1508, 6dr0 #4/C GLN 1696, 6dr0 #4/C VAL 1804, 6dr0 #4/C
VAL 2074, 6dr0 #4/C TYR 2225, 6dr0 #4/C PRO 2403, 6dr0 #4/C VAL 2611, 6dr0
#4/D GLN 76, 6dr0 #4/D TYR 323, 6dr0 #4/D ARG 527, 6dr0 #4/D LYS 674, 6dr0
#4/D ASP 893, 6dr0 #4/D PHE 1002, 6dr0 #4/D VAL 1038, 6dr0 #4/D VAL 1128, 6dr0
#4/D ASP 1423, 6dr0 #4/D PHE 1454, 6dr0 #4/D GLN 1696, 6dr0 #4/D VAL 1804,
6dr0 #4/D VAL 2074, 6dr0 #4/D TYR 2225, 6dr0 #4/D PRO 2403, 6dr0 #4/D VAL 2611
5518 hydrogen bonds
Adding 'H' to 6dr0 #4/A SER 5
Adding 'H' to 6dr0 #4/A ASP 86
Adding 'H' to 6dr0 #4/A LYS 351
Adding 'H' to 6dr0 #4/A GLU 690
Adding 'H' to 6dr0 #4/A ASP 961
59 messages similar to the above omitted
6dr0 #4/A VAL 2611 is not terminus, removing H atom from 'C'
6dr0 #4/B VAL 2611 is not terminus, removing H atom from 'C'
6dr0 #4/C VAL 2611 is not terminus, removing H atom from 'C'
6dr0 #4/D VAL 2611 is not terminus, removing H atom from 'C'
Termini for 6dqz (#3.2) chain A determined from SEQRES records
Termini for 6dqz (#3.2) chain B determined from SEQRES records
Termini for 6dqz (#3.2) chain D determined from SEQRES records
Termini for 6dqz (#3.2) chain C determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6dqz #3.2/A SER 5, 6dqz
#3.2/A ASP 86, 6dqz #3.2/A LYS 351, 6dqz #3.2/A PRO 534, 6dqz #3.2/A GLU 690,
6dqz #3.2/A ASP 961, 6dqz #3.2/A ASN 1024, 6dqz #3.2/A SER 1043, 6dqz #3.2/A
SER 1166, 6dqz #3.2/A THR 1463, 6dqz #3.2/A ALA 1490, 6dqz #3.2/A ALA 1515,
6dqz #3.2/A TRP 1718, 6dqz #3.2/A MET 1863, 6dqz #3.2/A GLU 2111, 6dqz #3.2/A
LEU 2231, 6dqz #3.2/A ASP 2449, 6dqz #3.2/B SER 5, 6dqz #3.2/B ASP 86, 6dqz
#3.2/B LYS 351, 6dqz #3.2/B PRO 534, 6dqz #3.2/B GLU 690, 6dqz #3.2/B ASP 961,
6dqz #3.2/B ASN 1024, 6dqz #3.2/B SER 1043, 6dqz #3.2/B SER 1166, 6dqz #3.2/B
THR 1463, 6dqz #3.2/B ALA 1490, 6dqz #3.2/B ALA 1515, 6dqz #3.2/B TRP 1718,
6dqz #3.2/B MET 1863, 6dqz #3.2/B GLU 2111, 6dqz #3.2/B LEU 2231, 6dqz #3.2/B
ASP 2449, 6dqz #3.2/D SER 5, 6dqz #3.2/D ASP 86, 6dqz #3.2/D GLU 348, 6dqz
#3.2/D GLY 533, 6dqz #3.2/D GLU 690, 6dqz #3.2/D ASP 961, 6dqz #3.2/D ASN
1024, 6dqz #3.2/D SER 1043, 6dqz #3.2/D SER 1166, 6dqz #3.2/D ALA 1434, 6dqz
#3.2/D LEU 1462, 6dqz #3.2/D ASP 1717, 6dqz #3.2/D MET 1863, 6dqz #3.2/D GLU
2111, 6dqz #3.2/D LEU 2231, 6dqz #3.2/D ASP 2449, 6dqz #3.2/C SER 5, 6dqz
#3.2/C ASP 86, 6dqz #3.2/C GLU 348, 6dqz #3.2/C GLY 533, 6dqz #3.2/C GLU 690,
6dqz #3.2/C ASP 961, 6dqz #3.2/C ASN 1024, 6dqz #3.2/C SER 1043, 6dqz #3.2/C
SER 1166, 6dqz #3.2/C ALA 1434, 6dqz #3.2/C LEU 1462, 6dqz #3.2/C ASP 1717,
6dqz #3.2/C MET 1863, 6dqz #3.2/C GLU 2111, 6dqz #3.2/C LEU 2231, 6dqz #3.2/C
ASP 2449
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 6dqz #3.2/A GLN 76, 6dqz
#3.2/A TYR 323, 6dqz #3.2/A ARG 527, 6dqz #3.2/A PRO 672, 6dqz #3.2/A ASP 893,
6dqz #3.2/A PRO 1003, 6dqz #3.2/A GLY 1037, 6dqz #3.2/A ASP 1129, 6dqz #3.2/A
ARG 1455, 6dqz #3.2/A PRO 1483, 6dqz #3.2/A ILE 1508, 6dqz #3.2/A GLN 1696,
6dqz #3.2/A VAL 1804, 6dqz #3.2/A VAL 2074, 6dqz #3.2/A TYR 2225, 6dqz #3.2/A
PRO 2403, 6dqz #3.2/A VAL 2611, 6dqz #3.2/B GLN 76, 6dqz #3.2/B TYR 323, 6dqz
#3.2/B ARG 527, 6dqz #3.2/B PRO 672, 6dqz #3.2/B ASP 893, 6dqz #3.2/B PRO
1003, 6dqz #3.2/B GLY 1037, 6dqz #3.2/B ASP 1129, 6dqz #3.2/B ARG 1455, 6dqz
#3.2/B PRO 1483, 6dqz #3.2/B ILE 1508, 6dqz #3.2/B GLN 1696, 6dqz #3.2/B VAL
1804, 6dqz #3.2/B VAL 2074, 6dqz #3.2/B TYR 2225, 6dqz #3.2/B PRO 2403, 6dqz
#3.2/B VAL 2611, 6dqz #3.2/D THR 77, 6dqz #3.2/D TYR 323, 6dqz #3.2/D ARG 527,
6dqz #3.2/D LYS 674, 6dqz #3.2/D ASP 893, 6dqz #3.2/D PHE 1002, 6dqz #3.2/D
VAL 1038, 6dqz #3.2/D VAL 1128, 6dqz #3.2/D ASP 1423, 6dqz #3.2/D PHE 1454,
6dqz #3.2/D GLN 1696, 6dqz #3.2/D VAL 1804, 6dqz #3.2/D VAL 2074, 6dqz #3.2/D
TYR 2225, 6dqz #3.2/D PRO 2403, 6dqz #3.2/D VAL 2611, 6dqz #3.2/C THR 77, 6dqz
#3.2/C TYR 323, 6dqz #3.2/C ARG 527, 6dqz #3.2/C LYS 674, 6dqz #3.2/C ASP 893,
6dqz #3.2/C PHE 1002, 6dqz #3.2/C VAL 1038, 6dqz #3.2/C VAL 1128, 6dqz #3.2/C
ASP 1423, 6dqz #3.2/C PHE 1454, 6dqz #3.2/C GLN 1696, 6dqz #3.2/C VAL 1804,
6dqz #3.2/C VAL 2074, 6dqz #3.2/C TYR 2225, 6dqz #3.2/C PRO 2403, 6dqz #3.2/C
VAL 2611
5725 hydrogen bonds
Adding 'H' to 6dqz #3.2/A SER 5
Adding 'H' to 6dqz #3.2/A ASP 86
Adding 'H' to 6dqz #3.2/A LYS 351
Adding 'H' to 6dqz #3.2/A GLU 690
Adding 'H' to 6dqz #3.2/A ASP 961
59 messages similar to the above omitted
6dqz #3.2/A VAL 2611 is not terminus, removing H atom from 'C'
6dqz #3.2/B VAL 2611 is not terminus, removing H atom from 'C'
6dqz #3.2/D VAL 2611 is not terminus, removing H atom from 'C'
6dqz #3.2/C VAL 2611 is not terminus, removing H atom from 'C'
307 hydrogens added
> isolde restrain ligands #3
> isolde restrain distances #3
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 363 residues in model #3.2 to IUPAC-IUB
standards.
> isolde adjust distances #3 displayThreshold 0.5
> select #3.2
139764 atoms, 141024 bonds, 71 pseudobonds, 8756 residues, 6 models selected
> isolde sim start sel
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Loading residue template for I3P from internal database
ISOLDE: stopped sim
Fetching CCD MET_LL from http://ligand-
expo.rcsb.org/reports/M/MET_LL/MET_LL.cif
Fetching CCD SER_LL_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif
Fetching CCD SER_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LSN3_DHG/SER_LSN3_DHG.cif
Fetching CCD CYS_LL_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif
Fetching CCD SER_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2_DHG/SER_LEO2_DHG.cif
Fetching CCD CYS_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LSN3_DHG/CYS_LSN3_DHG.cif
Fetching CCD SER_LFZW_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW_DHG/SER_LFZW_DHG.cif
Fetching CCD ASP_LL_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LL_DHD2/ASP_LL_DHD2.cif
Fetching CCD ASP_LL from http://ligand-
expo.rcsb.org/reports/A/ASP_LL/ASP_LL.cif
Fetching CCD CYS_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2_DHG/CYS_LEO2_DHG.cif
Fetching CCD ASP_LSN3_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LSN3_DHD2/ASP_LSN3_DHD2.cif
Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif
Fetching CCD PRO_LFZW from http://ligand-
expo.rcsb.org/reports/P/PRO_LFZW/PRO_LFZW.cif
Fetching CCD ORN from http://ligand-expo.rcsb.org/reports/O/ORN/ORN.cif
Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif
Fetching CCD VAL_LL from http://ligand-
expo.rcsb.org/reports/V/VAL_LL/VAL_LL.cif
Fetching CCD THR_LL_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LL_DHG1/THR_LL_DHG1.cif
Fetching CCD THR_LL from http://ligand-
expo.rcsb.org/reports/T/THR_LL/THR_LL.cif
Fetching CCD THR_LSN3_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LSN3_DHG1/THR_LSN3_DHG1.cif
Fetching CCD THR_LEO2_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2_DHG1/THR_LEO2_DHG1.cif
Fetching CCD THR_LEO2 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2/THR_LEO2.cif
Fetching CCD VAL_LEO2 from http://ligand-
expo.rcsb.org/reports/V/VAL_LEO2/VAL_LEO2.cif
Fetching CCD THR_LFZW_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW_DHG1/THR_LFZW_DHG1.cif
Fetching CCD THR_LFZW from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW/THR_LFZW.cif
Fetching CCD VAL_LFZW from http://ligand-
expo.rcsb.org/reports/V/VAL_LFZW/VAL_LFZW.cif
Fetching CCD ARG_LL from http://ligand-
expo.rcsb.org/reports/A/ARG_LL/ARG_LL.cif
Fetching CCD PRO_LL from http://ligand-
expo.rcsb.org/reports/P/PRO_LL/PRO_LL.cif
Deleted the following atoms from residue PRO D1547: H
Deleted the following atoms from residue PRO D1543: H
Deleted the following atoms from residue PRO D1494: H
Deleted the following atoms from residue PRO D1436: H
Deleted the following atoms from residue PRO C1547: H
Deleted the following atoms from residue PRO C1543: H
Deleted the following atoms from residue PRO C1494: H
Deleted the following atoms from residue PRO C1436: H
Deleted the following atoms from residue PRO B1547: H
Deleted the following atoms from residue PRO B1543: H
Deleted the following atoms from residue PRO B1501: H
Deleted the following atoms from residue PRO A1547: H
Deleted the following atoms from residue PRO A1543: H
Deleted the following atoms from residue PRO A1501: H
Fetching CCD GLN_LL from http://ligand-
expo.rcsb.org/reports/G/GLN_LL/GLN_LL.cif
Fetching CCD TYR_LL from http://ligand-
expo.rcsb.org/reports/T/TYR_LL/TYR_LL.cif
Fetching CCD PHE_LL from http://ligand-
expo.rcsb.org/reports/P/PHE_LL/PHE_LL.cif
Fetching CCD TRP_LL from http://ligand-
expo.rcsb.org/reports/T/TRP_LL/TRP_LL.cif
Fetching CCD GLU_LL_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LL_DHE2/GLU_LL_DHE2.cif
> select #3.2
142256 atoms, 143576 bonds, 71 pseudobonds, 8756 residues, 13 models selected
> isolde sim start sel
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 345 residues in model #3.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> fitmap #2 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 139459 atoms
average map value = 0.9744, steps = 44
shifted from previous position = 0.0135
rotated from previous position = 0.0045 degrees
atoms outside contour = 95881, contour level = 1.3524
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.04059068 -0.99874054 -0.02949130 417.37689222
0.99883773 0.04132708 -0.02480465 -1.76847035
0.02599220 -0.02845018 0.99925722 5.43650997
Axis -0.00182427 -0.02776462 0.99961282
Axis point 209.54634943 216.61760872 0.00000000
Rotation angle (degrees) 87.67386911
Shift along axis 4.72209774
> fitmap #2 inMap #5.3
Fit molecule 6dqs (#2) to map J981-DM.ccp4 (#5.3) using 139459 atoms
average map value = 0.9744, steps = 48
shifted from previous position = 0.0195
rotated from previous position = 0.00418 degrees
atoms outside contour = 95884, contour level = 1.3524
Position of 6dqs (#2) relative to J981-DM.ccp4 (#5.3) coordinates:
Matrix rotation and translation
0.04063040 -0.99874071 -0.02943079 417.34609067
0.99883593 0.04136546 -0.02481284 -1.77446747
0.02599901 -0.02838838 0.99925880 5.43826530
Axis -0.00178925 -0.02773780 0.99961363
Axis point 209.53383932 216.60694629 0.00000000
Rotation angle (degrees) 87.67158445
Shift along axis 4.73864911
> clipper associate #5.3 toModel #2
Opened J981-DM.ccp4 as #2.1.1.1, grid size 512,512,512, pixel 0.826, shown at
level 3.11, step 1, values float32
6dqs title:
Class 3 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor [more
info...]
Chain information for 6dqs
---
Chain | Description | UniProt
2.2/A 2.2/B 2.2/C 2.2/D | Inositol 1,4,5-trisphosphate receptor type 3 |
ITPR3_HUMAN
Non-standard residues in 6dqs #2.2
---
I3P — D-myo-inositol-1,4,5-triphosphate
ZN — zinc ion
> set bgColor white
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to 6dr0 #4/A MET 1491 CB because it is missing
heavy-atom bond partners
Not adding hydrogens to 6dr0 #4/A VAL 1492 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dr0 #4/A LYS 1494 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dr0 #4/A ARG 1496 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to 6dr0 #4/A ILE 1498 CB because it is missing heavy-atom
bond partners
271 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 6dr0 #4/A PRO 1543 N; 6dr0 #4/C PRO 1543 N; 6dr0 #4/B PRO 1547
N; 6dr0 #4/B PRO 1543 N; 6dr0 #4/A PRO 1547 N; 6dr0 #4/C PRO 1547 N; 6dr0 #4/A
PRO 1501 N; 6dr0 #4/D PRO 1436 N; 6dr0 #4/D PRO 1494 N; 6dr0 #4/D PRO 1543 N;
6dr0 #4/C PRO 1501 N; 6dr0 #4/B PRO 1501 N; 6dr0 #4/D PRO 1547 N
Not adding hydrogens to 6dqz #3.2/A HIS 1507 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 6dqz #3.2/B HIS 1507 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 6dqz #3.2/D HIS 1466 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 6dqz #3.2/D HIS 1500 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 6dqz #3.2/C HIS 1466 CB because it is missing heavy-
atom bond partners
357 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 6dqs #2.2/B PRO 1436 N; 6dqs #2.2/C PRO 1436 N; 6dqs #2.2/C PRO
1494 N; 6dqs #2.2/B PRO 1494 N; 6dqs #2.2/A PRO 1436 N; 6dqs #2.2/A PRO 1494
N; 6dqs #2.2/D PRO 1501 N; 6dqs #2.2/B PRO 1543 N; 6dqs #2.2/B PRO 1547 N;
6dqs #2.2/A PRO 1543 N; 6dqs #2.2/D PRO 1543 N; 6dqs #2.2/A PRO 1547 N; 6dqs
#2.2/C PRO 1543 N; 6dqs #2.2/D PRO 1547 N; 6dqs #2.2/C PRO 1547 N
notes | Termini for 6dr0 (#4) chain A determined from SEQRES records
Termini for 6dr0 (#4) chain B determined from SEQRES records
Termini for 6dr0 (#4) chain C determined from SEQRES records
Termini for 6dr0 (#4) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6dr0 #4/A SER 5, 6dr0
#4/A ASP 86, 6dr0 #4/A LYS 351, 6dr0 #4/A PRO 534, 6dr0 #4/A GLU 690, 6dr0
#4/A ASP 961, 6dr0 #4/A ASN 1024, 6dr0 #4/A SER 1043, 6dr0 #4/A SER 1166, 6dr0
#4/A THR 1463, 6dr0 #4/A ALA 1490, 6dr0 #4/A ALA 1515, 6dr0 #4/A TRP 1718,
6dr0 #4/A MET 1863, 6dr0 #4/A GLU 2111, 6dr0 #4/A LEU 2231, 6dr0 #4/A ASP
2449, 6dr0 #4/B SER 5, 6dr0 #4/B ASP 86, 6dr0 #4/B LYS 351, 6dr0 #4/B PRO 534,
6dr0 #4/B GLU 690, 6dr0 #4/B ASP 961, 6dr0 #4/B ASN 1024, 6dr0 #4/B SER 1043,
6dr0 #4/B SER 1166, 6dr0 #4/B THR 1463, 6dr0 #4/B ALA 1490, 6dr0 #4/B ALA
1515, 6dr0 #4/B TRP 1718, 6dr0 #4/B MET 1863, 6dr0 #4/B GLU 2111, 6dr0 #4/B
LEU 2231, 6dr0 #4/B ASP 2449, 6dr0 #4/C SER 5, 6dr0 #4/C ASP 86, 6dr0 #4/C GLU
348, 6dr0 #4/C GLY 533, 6dr0 #4/C GLU 690, 6dr0 #4/C ASP 961, 6dr0 #4/C ASN
1024, 6dr0 #4/C SER 1043, 6dr0 #4/C SER 1166, 6dr0 #4/C THR 1463, 6dr0 #4/C
ALA 1490, 6dr0 #4/C ALA 1515, 6dr0 #4/C TRP 1718, 6dr0 #4/C MET 1863, 6dr0
#4/C GLU 2111, 6dr0 #4/C LEU 2231, 6dr0 #4/C ASP 2449, 6dr0 #4/D SER 5, 6dr0
#4/D ASP 86, 6dr0 #4/D LYS 351, 6dr0 #4/D PRO 534, 6dr0 #4/D GLU 690, 6dr0
#4/D ASP 961, 6dr0 #4/D ASN 1024, 6dr0 #4/D SER 1043, 6dr0 #4/D SER 1166, 6dr0
#4/D ALA 1434, 6dr0 #4/D LEU 1462, 6dr0 #4/D ASP 1717, 6dr0 #4/D MET 1863,
6dr0 #4/D GLU 2111, 6dr0 #4/D LEU 2231, 6dr0 #4/D ASP 2449
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 6dr0 #4/A GLN 76, 6dr0
#4/A TYR 323, 6dr0 #4/A ARG 527, 6dr0 #4/A PRO 672, 6dr0 #4/A ASP 893, 6dr0
#4/A PRO 1003, 6dr0 #4/A GLY 1037, 6dr0 #4/A ASP 1129, 6dr0 #4/A ARG 1455,
6dr0 #4/A PRO 1483, 6dr0 #4/A ILE 1508, 6dr0 #4/A GLN 1696, 6dr0 #4/A VAL
1804, 6dr0 #4/A VAL 2074, 6dr0 #4/A TYR 2225, 6dr0 #4/A PRO 2403, 6dr0 #4/A
VAL 2611, 6dr0 #4/B GLN 76, 6dr0 #4/B TYR 323, 6dr0 #4/B ARG 527, 6dr0 #4/B
PRO 672, 6dr0 #4/B ASP 893, 6dr0 #4/B PRO 1003, 6dr0 #4/B GLY 1037, 6dr0 #4/B
ASP 1129, 6dr0 #4/B ARG 1455, 6dr0 #4/B PRO 1483, 6dr0 #4/B ILE 1508, 6dr0
#4/B GLN 1696, 6dr0 #4/B VAL 1804, 6dr0 #4/B VAL 2074, 6dr0 #4/B TYR 2225,
6dr0 #4/B PRO 2403, 6dr0 #4/B VAL 2611, 6dr0 #4/C THR 77, 6dr0 #4/C TYR 323,
6dr0 #4/C ARG 527, 6dr0 #4/C PRO 672, 6dr0 #4/C ASP 893, 6dr0 #4/C PRO 1003,
6dr0 #4/C GLY 1037, 6dr0 #4/C ASP 1129, 6dr0 #4/C ARG 1455, 6dr0 #4/C PRO
1483, 6dr0 #4/C ILE 1508, 6dr0 #4/C GLN 1696, 6dr0 #4/C VAL 1804, 6dr0 #4/C
VAL 2074, 6dr0 #4/C TYR 2225, 6dr0 #4/C PRO 2403, 6dr0 #4/C VAL 2611, 6dr0
#4/D GLN 76, 6dr0 #4/D TYR 323, 6dr0 #4/D ARG 527, 6dr0 #4/D LYS 674, 6dr0
#4/D ASP 893, 6dr0 #4/D PHE 1002, 6dr0 #4/D VAL 1038, 6dr0 #4/D VAL 1128, 6dr0
#4/D ASP 1423, 6dr0 #4/D PHE 1454, 6dr0 #4/D GLN 1696, 6dr0 #4/D VAL 1804,
6dr0 #4/D VAL 2074, 6dr0 #4/D TYR 2225, 6dr0 #4/D PRO 2403, 6dr0 #4/D VAL 2611
5507 hydrogen bonds
6dr0 #4/A VAL 2611 is not terminus, removing H atom from 'C'
6dr0 #4/B VAL 2611 is not terminus, removing H atom from 'C'
6dr0 #4/C VAL 2611 is not terminus, removing H atom from 'C'
6dr0 #4/D VAL 2611 is not terminus, removing H atom from 'C'
Termini for 6dqz (#3.2) chain A determined from SEQRES records
Termini for 6dqz (#3.2) chain B determined from SEQRES records
Termini for 6dqz (#3.2) chain D determined from SEQRES records
Termini for 6dqz (#3.2) chain C determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6dqz #3.2/A SER 5, 6dqz
#3.2/A ASP 86, 6dqz #3.2/A LYS 351, 6dqz #3.2/A PRO 534, 6dqz #3.2/A GLU 690,
6dqz #3.2/A ASP 961, 6dqz #3.2/A ASN 1024, 6dqz #3.2/A SER 1043, 6dqz #3.2/A
SER 1166, 6dqz #3.2/A THR 1463, 6dqz #3.2/A ALA 1490, 6dqz #3.2/A ALA 1515,
6dqz #3.2/A TRP 1718, 6dqz #3.2/A MET 1863, 6dqz #3.2/A GLU 2111, 6dqz #3.2/A
LEU 2231, 6dqz #3.2/A ASP 2449, 6dqz #3.2/B SER 5, 6dqz #3.2/B ASP 86, 6dqz
#3.2/B LYS 351, 6dqz #3.2/B PRO 534, 6dqz #3.2/B GLU 690, 6dqz #3.2/B ASP 961,
6dqz #3.2/B ASN 1024, 6dqz #3.2/B SER 1043, 6dqz #3.2/B SER 1166, 6dqz #3.2/B
THR 1463, 6dqz #3.2/B ALA 1490, 6dqz #3.2/B ALA 1515, 6dqz #3.2/B TRP 1718,
6dqz #3.2/B MET 1863, 6dqz #3.2/B GLU 2111, 6dqz #3.2/B LEU 2231, 6dqz #3.2/B
ASP 2449, 6dqz #3.2/D SER 5, 6dqz #3.2/D ASP 86, 6dqz #3.2/D GLU 348, 6dqz
#3.2/D GLY 533, 6dqz #3.2/D GLU 690, 6dqz #3.2/D ASP 961, 6dqz #3.2/D ASN
1024, 6dqz #3.2/D SER 1043, 6dqz #3.2/D SER 1166, 6dqz #3.2/D ALA 1434, 6dqz
#3.2/D LEU 1462, 6dqz #3.2/D ASP 1717, 6dqz #3.2/D MET 1863, 6dqz #3.2/D GLU
2111, 6dqz #3.2/D LEU 2231, 6dqz #3.2/D ASP 2449, 6dqz #3.2/C SER 5, 6dqz
#3.2/C ASP 86, 6dqz #3.2/C GLU 348, 6dqz #3.2/C GLY 533, 6dqz #3.2/C GLU 690,
6dqz #3.2/C ASP 961, 6dqz #3.2/C ASN 1024, 6dqz #3.2/C SER 1043, 6dqz #3.2/C
SER 1166, 6dqz #3.2/C ALA 1434, 6dqz #3.2/C LEU 1462, 6dqz #3.2/C ASP 1717,
6dqz #3.2/C MET 1863, 6dqz #3.2/C GLU 2111, 6dqz #3.2/C LEU 2231, 6dqz #3.2/C
ASP 2449
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 6dqz #3.2/A GLN 76, 6dqz
#3.2/A TYR 323, 6dqz #3.2/A ARG 527, 6dqz #3.2/A PRO 672, 6dqz #3.2/A ASP 893,
6dqz #3.2/A PRO 1003, 6dqz #3.2/A GLY 1037, 6dqz #3.2/A ASP 1129, 6dqz #3.2/A
ARG 1455, 6dqz #3.2/A PRO 1483, 6dqz #3.2/A ILE 1508, 6dqz #3.2/A GLN 1696,
6dqz #3.2/A VAL 1804, 6dqz #3.2/A VAL 2074, 6dqz #3.2/A TYR 2225, 6dqz #3.2/A
PRO 2403, 6dqz #3.2/A VAL 2611, 6dqz #3.2/B GLN 76, 6dqz #3.2/B TYR 323, 6dqz
#3.2/B ARG 527, 6dqz #3.2/B PRO 672, 6dqz #3.2/B ASP 893, 6dqz #3.2/B PRO
1003, 6dqz #3.2/B GLY 1037, 6dqz #3.2/B ASP 1129, 6dqz #3.2/B ARG 1455, 6dqz
#3.2/B PRO 1483, 6dqz #3.2/B ILE 1508, 6dqz #3.2/B GLN 1696, 6dqz #3.2/B VAL
1804, 6dqz #3.2/B VAL 2074, 6dqz #3.2/B TYR 2225, 6dqz #3.2/B PRO 2403, 6dqz
#3.2/B VAL 2611, 6dqz #3.2/D THR 77, 6dqz #3.2/D TYR 323, 6dqz #3.2/D ARG 527,
6dqz #3.2/D LYS 674, 6dqz #3.2/D ASP 893, 6dqz #3.2/D PHE 1002, 6dqz #3.2/D
VAL 1038, 6dqz #3.2/D VAL 1128, 6dqz #3.2/D ASP 1423, 6dqz #3.2/D PHE 1454,
6dqz #3.2/D GLN 1696, 6dqz #3.2/D VAL 1804, 6dqz #3.2/D VAL 2074, 6dqz #3.2/D
TYR 2225, 6dqz #3.2/D PRO 2403, 6dqz #3.2/D VAL 2611, 6dqz #3.2/C THR 77, 6dqz
#3.2/C TYR 323, 6dqz #3.2/C ARG 527, 6dqz #3.2/C LYS 674, 6dqz #3.2/C ASP 893,
6dqz #3.2/C PHE 1002, 6dqz #3.2/C VAL 1038, 6dqz #3.2/C VAL 1128, 6dqz #3.2/C
ASP 1423, 6dqz #3.2/C PHE 1454, 6dqz #3.2/C GLN 1696, 6dqz #3.2/C VAL 1804,
6dqz #3.2/C VAL 2074, 6dqz #3.2/C TYR 2225, 6dqz #3.2/C PRO 2403, 6dqz #3.2/C
VAL 2611
9004 hydrogen bonds
6dqz #3.2/A VAL 2611 is not terminus, removing H atom from 'C'
6dqz #3.2/B VAL 2611 is not terminus, removing H atom from 'C'
6dqz #3.2/D VAL 2611 is not terminus, removing H atom from 'C'
6dqz #3.2/C VAL 2611 is not terminus, removing H atom from 'C'
Termini for 6dqs (#2.2) chain A determined from SEQRES records
Termini for 6dqs (#2.2) chain B determined from SEQRES records
Termini for 6dqs (#2.2) chain C determined from SEQRES records
Termini for 6dqs (#2.2) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 6dqs #2.2/A SER 5, 6dqs
#2.2/A ASP 86, 6dqs #2.2/A GLU 348, 6dqs #2.2/A GLY 533, 6dqs #2.2/A GLU 690,
6dqs #2.2/A ASP 961, 6dqs #2.2/A ASN 1024, 6dqs #2.2/A SER 1043, 6dqs #2.2/A
SER 1166, 6dqs #2.2/A ALA 1434, 6dqs #2.2/A LEU 1462, 6dqs #2.2/A ASP 1717,
6dqs #2.2/A MET 1863, 6dqs #2.2/A GLU 2111, 6dqs #2.2/A LEU 2231, 6dqs #2.2/A
ASP 2449, 6dqs #2.2/B SER 5, 6dqs #2.2/B ASP 86, 6dqs #2.2/B GLU 348, 6dqs
#2.2/B GLY 533, 6dqs #2.2/B GLU 690, 6dqs #2.2/B ASP 961, 6dqs #2.2/B ASN
1024, 6dqs #2.2/B SER 1043, 6dqs #2.2/B SER 1166, 6dqs #2.2/B ALA 1434, 6dqs
#2.2/B LEU 1462, 6dqs #2.2/B ASP 1717, 6dqs #2.2/B MET 1863, 6dqs #2.2/B GLU
2111, 6dqs #2.2/B LEU 2231, 6dqs #2.2/B ASP 2449, 6dqs #2.2/C SER 5, 6dqs
#2.2/C ASP 86, 6dqs #2.2/C GLU 348, 6dqs #2.2/C GLY 533, 6dqs #2.2/C GLU 690,
6dqs #2.2/C ASP 961, 6dqs #2.2/C ASN 1024, 6dqs #2.2/C SER 1043, 6dqs #2.2/C
SER 1166, 6dqs #2.2/C ALA 1434, 6dqs #2.2/C LEU 1462, 6dqs #2.2/C ASP 1717,
6dqs #2.2/C MET 1863, 6dqs #2.2/C GLU 2111, 6dqs #2.2/C LEU 2231, 6dqs #2.2/C
ASP 2449, 6dqs #2.2/D SER 5, 6dqs #2.2/D ASP 86, 6dqs #2.2/D GLU 348, 6dqs
#2.2/D GLY 533, 6dqs #2.2/D GLU 690, 6dqs #2.2/D ASP 961, 6dqs #2.2/D ASN
1024, 6dqs #2.2/D SER 1043, 6dqs #2.2/D SER 1166, 6dqs #2.2/D THR 1463, 6dqs
#2.2/D ALA 1490, 6dqs #2.2/D ALA 1515, 6dqs #2.2/D TRP 1718, 6dqs #2.2/D MET
1863, 6dqs #2.2/D GLU 2111, 6dqs #2.2/D LEU 2231, 6dqs #2.2/D ASP 2449
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 6dqs #2.2/A THR 77, 6dqs
#2.2/A TYR 323, 6dqs #2.2/A ARG 527, 6dqs #2.2/A LYS 674, 6dqs #2.2/A ASP 893,
6dqs #2.2/A PHE 1002, 6dqs #2.2/A VAL 1038, 6dqs #2.2/A VAL 1128, 6dqs #2.2/A
ASP 1423, 6dqs #2.2/A PHE 1454, 6dqs #2.2/A GLN 1696, 6dqs #2.2/A VAL 1804,
6dqs #2.2/A VAL 2074, 6dqs #2.2/A TYR 2225, 6dqs #2.2/A PRO 2403, 6dqs #2.2/A
VAL 2611, 6dqs #2.2/B THR 77, 6dqs #2.2/B TYR 323, 6dqs #2.2/B ARG 527, 6dqs
#2.2/B LYS 674, 6dqs #2.2/B ASP 893, 6dqs #2.2/B PHE 1002, 6dqs #2.2/B VAL
1038, 6dqs #2.2/B VAL 1128, 6dqs #2.2/B ASP 1423, 6dqs #2.2/B PHE 1454, 6dqs
#2.2/B GLN 1696, 6dqs #2.2/B VAL 1804, 6dqs #2.2/B VAL 2074, 6dqs #2.2/B TYR
2225, 6dqs #2.2/B PRO 2403, 6dqs #2.2/B VAL 2611, 6dqs #2.2/C THR 77, 6dqs
#2.2/C TYR 323, 6dqs #2.2/C ARG 527, 6dqs #2.2/C LYS 674, 6dqs #2.2/C ASP 893,
6dqs #2.2/C PHE 1002, 6dqs #2.2/C VAL 1038, 6dqs #2.2/C VAL 1128, 6dqs #2.2/C
ASP 1423, 6dqs #2.2/C PHE 1454, 6dqs #2.2/C GLN 1696, 6dqs #2.2/C VAL 1804,
6dqs #2.2/C VAL 2074, 6dqs #2.2/C TYR 2225, 6dqs #2.2/C PRO 2403, 6dqs #2.2/C
VAL 2611, 6dqs #2.2/D THR 77, 6dqs #2.2/D TYR 323, 6dqs #2.2/D ARG 527, 6dqs
#2.2/D PRO 672, 6dqs #2.2/D ASP 893, 6dqs #2.2/D PHE 1002, 6dqs #2.2/D GLY
1037, 6dqs #2.2/D ASP 1129, 6dqs #2.2/D ARG 1455, 6dqs #2.2/D PRO 1483, 6dqs
#2.2/D ILE 1508, 6dqs #2.2/D GLN 1696, 6dqs #2.2/D VAL 1804, 6dqs #2.2/D VAL
2074, 6dqs #2.2/D TYR 2225, 6dqs #2.2/D PRO 2403, 6dqs #2.2/D VAL 2611
5497 hydrogen bonds
6dqs #2.2/A VAL 2611 is not terminus, removing H atom from 'C'
6dqs #2.2/B VAL 2611 is not terminus, removing H atom from 'C'
6dqs #2.2/C VAL 2611 is not terminus, removing H atom from 'C'
6dqs #2.2/D VAL 2611 is not terminus, removing H atom from 'C'
0 hydrogens added
> isolde restrain ligands #2
> isolde restrain distances #2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 362 residues in model #2.2 to IUPAC-IUB
standards.
> isolde adjust distances #2 displayThreshold 0.5
> hide #!3 models
> show #!2.2 models
> select #2.2
139459 atoms, 140709 bonds, 76 pseudobonds, 8758 residues, 6 models selected
> isolde sim start sel
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
Deleted the following atoms from residue PRO D1547: H
Deleted the following atoms from residue PRO D1543: H
Deleted the following atoms from residue PRO D1501: H
Deleted the following atoms from residue PRO C1547: H
Deleted the following atoms from residue PRO C1543: H
Deleted the following atoms from residue PRO C1494: H
Deleted the following atoms from residue PRO C1436: H
Deleted the following atoms from residue PRO B1547: H
Deleted the following atoms from residue PRO B1543: H
Deleted the following atoms from residue PRO B1494: H
Deleted the following atoms from residue PRO B1436: H
Deleted the following atoms from residue PRO A1547: H
Deleted the following atoms from residue PRO A1543: H
Deleted the following atoms from residue PRO A1494: H
Deleted the following atoms from residue PRO A1436: H
> select #2.2
142233 atoms, 143547 bonds, 76 pseudobonds, 8758 residues, 13 models selected
> isolde sim start sel
ISOLDE: started sim
> select clear
Traceback (most recent call last):
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/Users/navid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1276, in
_mdff_global_k_change_cb
self.sim_handler.set_mdff_global_k(mgr.volume, k)
File "/Users/navid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 2606, in
set_mdff_global_k
f.set_global_k(k, context = context)
File "/Users/navid/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 241, in set_global_k
context.setParameter(self._global_k_name, k)
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2297, in setParameter
return _openmm.Context_setParameter(self, name, value)
openmm.OpenMMException: Called setParameter() with invalid parameter name:
mdff_global_k_1
Error processing trigger "global k changed":
openmm.OpenMMException: Called setParameter() with invalid parameter name:
mdff_global_k_1
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2297, in setParameter
return _openmm.Context_setParameter(self, name, value)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Ultra
OpenGL vendor: Apple
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac13,2
Model Number: Z14K000APLL/A
Chip: Unknown
Total Number of Cores: 20 (16 performance and 4 efficiency)
Memory: 128 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 33 days, 17 hours, 2 minutes
Graphics/Displays:
Apple M1 Ultra:
Chipset Model: Apple M1 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 64
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG UltraFine:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
LG UltraFine:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → "select clear" during simulation: Called setParameter() with invalid parameter name |
follow-up: 2 comment:2 by , 3 years ago
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Hmm... that's an odd one. Nothing to do with the "select clear" - that was just the last command that happened to be logged. They've tried to change the MDFF weight on a map (presumably via the ISOLDE GUI "Noncrystallographic map settings" dialogue... this is done by changing the corresponding parameter `mdff_global_k_{map index}` in the simulation context, which is created when the MDFF force is. I honestly have *no* idea how this error could have come about. On Fri, Mar 31, 2023 at 9:54 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: