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Opened 3 years ago
Closed 3 years ago
#7348 closed defect (duplicate)
KeyError deleting 2D arrow
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Linux-4.18.0-348.20.1.el8_5.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
I am not able to run "2dlabels delete all" command after I create some 2dlabels and 2d arrows.
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A1_bin2/f107_A1_session_fly_base.cxs format session
Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
step 1, values int8
Log from Fri Jul 29 15:52:14 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs format session
Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
step 1, values int8
Log from Fri Jul 29 13:26:07 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> ~display #2-5
> volume #2-5 show style surface
> ~display #2-5
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1700
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:08:40 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:27:32 2022 ———
opened ChimeraX session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1700
> volume #1 hide
> wait 1
> volume #2-5 region all
> wait 1
> volume #3-5 transparency 0
> volume #2 transparency 0.6
> zoom 0.85
> wait 5
> roll y 1 360
> wait
executed F107-A3_session.cxc
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> ~display #2-5
> volume #2-5 show style surface
> ~display #2-5
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1700
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:08:40 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:27:32 2022 ———
opened ChimeraX session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1743
> volume #1 hide
> wait 1
> volume #2-5 region all
> wait 1
> volume #3-5 transparency 0
> volume #2 transparency 0.6
executed F107-A3_session.cxc
> zoom 0.85
> wait 5
> oll y 1 360; wait;
Unknown command: oll y 1 360; wait;
> roll y 1 360
> wait
> fly p1 p2 100
> wait
> view p1
> roll y 1 360
> wait
> fly p1 p2 100
> wait
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> ~display #2-5
> volume #2-5 show style surface
> ~display #2-5
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1700
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:08:40 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:27:32 2022 ———
opened ChimeraX session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1743
> volume #1 hide
> wait 1
> volume #2-5 region all
> wait 1
> volume #3-5 transparency 0
> volume #2 transparency 0.6
> roll y 1 360
> wait
> fly p1 p2 100
> wait
executed F107-A3_session.cxc
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> ~display #2-5
> volume #2-5 show style surface
> ~display #2-5
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1700
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
[deleted much of the log to fit within ticket length limits]
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:08:40 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:27:32 2022 ———
opened ChimeraX session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxc
> movie record supersample 3
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1743
> volume #1 hide
> wait 1
> volume #2-5 region all
> wait 1
> volume #3-5 transparency 0
> volume #2 transparency 0.6
> roll y 1 360
> wait
> fly p1 p2 100
> wait
> perframe "volume all region 0,0,0,2129,1523,$1" ranges 1743,30
> wait 1720
> movie encode framerate 25 quality good output
> /tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4 verbose true
> format h264 wait true
/usr/libexec/UCSF-ChimeraX/bin/ffmpeg -r 25.0 -i /tmp/chimovie_mNsA-%05d.ppm
-vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4
-pix_fmt yuv420p -crf 20
/tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with gcc 8 (GCC)
configuration: --prefix=/tmp/chx-v1.4.jOWCxR/build --enable-gpl --enable-
version3 --disable-network --disable-doc --disable-devices --disable-ffplay
--disable-ffserver --disable-ffprobe --enable-libtheora --enable-libvpx
--enable-libx264 --yasmexe=/tmp/chx-v1.4.jOWCxR/build/bin/yasm --optflags=-O
--extra-cflags=-I/tmp/chx-v1.4.jOWCxR/build/include --extra-ldflags='-O3 -Wall
-Wextra -D_FORTIFY=2 -L/tmp/chx-v1.4.jOWCxR/build/lib' --extra-libs=-ldl
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from '/tmp/chimovie_mNsA-%05d.ppm':
Duration: 00:02:41.16, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1708x1033, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 0x2f41260] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
FMA3 AVX2 LZCNT BMI2
[libx264 @ 0x2f41260] profile High, level 4.0
[libx264 @ 0x2f41260] 264 - core 148 - H.264/MPEG-4 AVC codec - Copyleft
2003-2017 - http://www.videolan.org/x264.html - options: cabac=1 ref=3
deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00
mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11
fast_pskip=1 chroma_qp_offset=-2 threads=32 lookahead_threads=5
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to
'/tmp/imprima/F107A3_bin2/movies/F107-A3_full_bin2_srv.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1708x1032, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 74 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 156 fps=155 q=25.0 size= 1664kB time=00:00:03.08 bitrate=4426.1kbits/s
speed=3.06x frame= 230 fps=152 q=25.0 size= 6025kB time=00:00:06.04
bitrate=8171.4kbits/s speed=3.99x frame= 317 fps=157 q=25.0 size= 12658kB
time=00:00:09.52 bitrate=10891.7kbits/s speed=4.73x frame= 404 fps=161 q=25.0
size= 18823kB time=00:00:13.00 bitrate=11861.3kbits/s speed=5.17x frame= 482
fps=160 q=25.0 size= 24254kB time=00:00:16.12 bitrate=12325.6kbits/s
speed=5.35x frame= 569 fps=162 q=25.0 size= 30513kB time=00:00:19.60
bitrate=12753.0kbits/s speed=5.57x frame= 656 fps=162 q=25.0 size= 36817kB
time=00:00:23.08 bitrate=13067.8kbits/s speed= 5.7x frame= 744 fps=164 q=25.0
size= 43111kB time=00:00:26.60 bitrate=13276.7kbits/s speed=5.85x frame= 833
fps=165 q=25.0 size= 49483kB time=00:00:30.16 bitrate=13440.4kbits/s
speed=5.97x frame= 917 fps=165 q=25.0 size= 55575kB time=00:00:33.52
bitrate=13582.0kbits/s speed=6.04x frame= 1006 fps=166 q=25.0 size= 61701kB
time=00:00:37.08 bitrate=13631.5kbits/s speed=6.12x frame= 1091 fps=166 q=25.0
size= 67214kB time=00:00:40.48 bitrate=13602.1kbits/s speed=6.17x frame= 1180
fps=167 q=25.0 size= 72771kB time=00:00:44.04 bitrate=13536.4kbits/s
speed=6.24x frame= 1269 fps=168 q=25.0 size= 78098kB time=00:00:47.60
bitrate=13440.7kbits/s speed=6.29x frame= 1353 fps=168 q=25.0 size= 82790kB
time=00:00:50.96 bitrate=13308.7kbits/s speed=6.32x frame= 1442 fps=168 q=25.0
size= 87426kB time=00:00:54.52 bitrate=13136.4kbits/s speed=6.36x frame= 1532
fps=169 q=25.0 size= 91864kB time=00:00:58.12 bitrate=12948.3kbits/s speed=
6.4x frame= 1617 fps=169 q=25.0 size= 95915kB time=00:01:01.52
bitrate=12772.1kbits/s speed=6.42x frame= 1706 fps=169 q=25.0 size= 99937kB
time=00:01:05.08 bitrate=12579.7kbits/s speed=6.45x frame= 1795 fps=170 q=25.0
size= 103922kB time=00:01:08.64 bitrate=12402.8kbits/s speed=6.48x frame= 1878
fps=169 q=25.0 size= 107590kB time=00:01:11.96 bitrate=12248.1kbits/s
speed=6.49x frame= 1966 fps=170 q=25.0 size= 110849kB time=00:01:15.48
bitrate=12030.7kbits/s speed=6.51x frame= 2054 fps=170 q=25.0 size= 116186kB
time=00:01:19.00 bitrate=12048.1kbits/s speed=6.53x frame= 2142 fps=170 q=25.0
size= 121307kB time=00:01:22.52 bitrate=12042.5kbits/s speed=6.55x frame= 2230
fps=170 q=25.0 size= 127266kB time=00:01:26.04 bitrate=12117.2kbits/s
speed=6.57x frame= 2318 fps=170 q=25.0 size= 131561kB time=00:01:29.56
bitrate=12033.8kbits/s speed=6.59x frame= 2405 fps=171 q=25.0 size= 134057kB
time=00:01:33.04 bitrate=11803.4kbits/s speed= 6.6x frame= 2494 fps=171 q=25.0
size= 135297kB time=00:01:36.60 bitrate=11473.6kbits/s speed=6.62x frame= 2584
fps=171 q=25.0 size= 136340kB time=00:01:40.20 bitrate=11146.7kbits/s
speed=6.63x frame= 2667 fps=171 q=25.0 size= 137370kB time=00:01:43.52
bitrate=10870.7kbits/s speed=6.63x frame= 2749 fps=171 q=25.0 size= 138613kB
time=00:01:46.80 bitrate=10632.2kbits/s speed=6.63x frame= 2830 fps=170 q=25.0
size= 139607kB time=00:01:50.04 bitrate=10393.1kbits/s speed=6.62x frame= 2910
fps=170 q=25.0 size= 140624kB time=00:01:53.24 bitrate=10173.0kbits/s
speed=6.61x frame= 2994 fps=170 q=25.0 size= 141666kB time=00:01:56.60
bitrate=9953.0kbits/s speed=6.61x frame= 3078 fps=170 q=25.0 size= 142646kB
time=00:01:59.96 bitrate=9741.2kbits/s speed=6.62x frame= 3167 fps=170 q=25.0
size= 143594kB time=00:02:03.52 bitrate=9523.3kbits/s speed=6.63x frame= 3254
fps=170 q=25.0 size= 144663kB time=00:02:07.00 bitrate=9331.4kbits/s
speed=6.64x frame= 3345 fps=170 q=25.0 size= 145501kB time=00:02:10.64
bitrate=9123.9kbits/s speed=6.65x frame= 3436 fps=171 q=25.0 size= 146505kB
time=00:02:14.28 bitrate=8937.8kbits/s speed=6.67x frame= 3527 fps=171 q=25.0
size= 147412kB time=00:02:17.92 bitrate=8755.8kbits/s speed=6.68x frame= 3618
fps=171 q=25.0 size= 148221kB time=00:02:21.56 bitrate=8577.5kbits/s
speed=6.69x frame= 3709 fps=171 q=25.0 size= 149054kB time=00:02:25.20
bitrate=8409.4kbits/s speed=6.71x frame= 3800 fps=172 q=25.0 size= 149760kB
time=00:02:28.84 bitrate=8242.7kbits/s speed=6.72x frame= 3891 fps=172 q=25.0
size= 150377kB time=00:02:32.48 bitrate=8079.0kbits/s speed=6.73x frame= 3982
fps=172 q=25.0 size= 151132kB time=00:02:36.12 bitrate=7930.3kbits/s
speed=6.74x frame= 4029 fps=171 q=-1.0 Lsize= 152060kB time=00:02:41.04
bitrate=7735.2kbits/s speed=6.85x
video:152015kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.029385%
[libx264 @ 0x2f41260] frame I:18 Avg QP:11.68 size:146649
[libx264 @ 0x2f41260] frame P:1617 Avg QP:18.50 size: 44842
[libx264 @ 0x2f41260] frame B:2394 Avg QP:23.32 size: 33631
[libx264 @ 0x2f41260] consecutive B-frames: 16.9% 7.5% 12.4% 63.1%
[libx264 @ 0x2f41260] mb I I16..4: 52.0% 30.2% 17.8%
[libx264 @ 0x2f41260] mb P I16..4: 1.1% 3.0% 1.6% P16..4: 7.9% 4.3% 4.4% 0.0%
0.0% skip:77.7%
[libx264 @ 0x2f41260] mb B I16..4: 0.3% 1.2% 0.6% B16..8: 9.2% 3.0% 1.5%
direct: 5.0% skip:79.1% L0:34.0% L1:38.4% BI:27.6%
[libx264 @ 0x2f41260] 8x8 transform intra:51.8% inter:33.7%
[libx264 @ 0x2f41260] coded y,uvDC,uvAC intra: 70.6% 35.1% 31.0% inter: 10.9%
6.3% 4.1%
[libx264 @ 0x2f41260] i16 v,h,dc,p: 68% 29% 3% 1%
[libx264 @ 0x2f41260] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 6% 39% 7% 7% 9% 5% 8%
7%
[libx264 @ 0x2f41260] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 9% 20% 9% 9% 12% 8%
10% 8%
[libx264 @ 0x2f41260] i8c dc,h,v,p: 70% 13% 16% 2%
[libx264 @ 0x2f41260] Weighted P-Frames: Y:0.1% UV:0.1%
[libx264 @ 0x2f41260] ref P L0: 72.3% 12.7% 9.9% 5.1% 0.0%
[libx264 @ 0x2f41260] ref B L0: 89.2% 8.1% 2.6%
[libx264 @ 0x2f41260] ref B L1: 97.6% 2.4%
[libx264 @ 0x2f41260] kb/s:7727.11
Movie saved to /tmp/imprima/.../movies/F107-A3_full_bin2_srv.mp4
executed F107-A3_session.cxc
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
Log from Wed Jul 27 14:27:32 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> ~display #2-5
> volume #2-5 show style surface
> ~display #2-5
> fly p2 p1 100
> wait
> volume #2-5 show style surface transparency 0.5
> 2dlabels text Nuclei color #5555ff size 18 xpos .03 ypos .92 bold true
> bgColor black margin 5
> 2dlabels text Mitochondria color #aa557f size 18 xpos .03 ypos .87 bold true
> bgColor black margin 5
> 2dlabels text "Actin bundles" color #f514fd size 18 xpos .03 ypos .82 bold
> true bgColor black margin 5
> 2dlabels text "Cell junctions" color #11ffcc size 18 xpos .03 ypos .77 bold
> true bgColor black margin 5
> volume all planes z,1743,30
> wait 1700
> close session
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs format session
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 1, values int8
Log from Wed Jul 27 14:08:40 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 2, values int8
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 3, values int8
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at level 0.8, step 2, values int8
Log from Wed Jul 27 13:49:38 2022You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /tmp/imprima/F107A3_bin2/data/f107a3_flipz.mrc
Opened f107a3_flipz.mrc as #1, grid size 2130,1524,1749, pixel 300, shown at
step 1, values int8
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,2129,1523,1748 step 2 colorMode opaque8 imageMode
> "box faces"
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #1 region 0,0,0,1385,1409,1604
> volume #1 region all
> volume #1 region 0,0,0,2129,1523,1748
> view orient
> zoom 0.85
> view name p1
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> close #2
> open /tmp/imprima/F107A3_bin2/data/nuclei_f107a3_flipz.mrc
Opened nuclei_f107a3_flipz.mrc as #2, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/mitos_f107a3_flipz.mrc
Opened mitos_f107a3_flipz.mrc as #3, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/actin_f107a3_flipz.mrc
Opened actin_f107a3_flipz.mrc as #4, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> open /tmp/imprima/F107A3_bin2/data/junctions_f107a3_flipz.mrc
Opened junctions_f107a3_flipz.mrc as #5, grid size 2130,1524,1749, pixel 300,
shown at step 1, values int8
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #1 region 0,0,0,2129,1523,1740
> volume all region 0,0,0,2129,1523,1740
> volume #5 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #4 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #3 region 0,0,0,2129,1523,1740 step 2 colorMode opaque8
> showOutlineBox true imageMode "box faces"
> volume #2 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #2 show style surface level -50 color #5555ff
> volume #2 show style surface level 10 color #5555ff
> lighting soft
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> volume #2 show style surface level 0.8 color #5555ff
> volume #3 show style surface level 0.8 color #aa557f
> volume #4 show style surface level 0.8 color #f514fd
> volume #5 show style surface level 0.8 color #11ffcc
> ~display #1
> volume #2 transparency 0.6
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> display #1
> volume all region 0,0,0,2129,1523,1744
> ~display #1
> volume #2 show style surface step 2
> volume #3 show style surface step 3
> volume #4 show style surface step 2
> volume #5 show style surface step 2
> volume #5 show style surface step 1
> volume #5 show style surface step 2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> view name p2
> view list
Named views: p1, p2
> view p1
> view p2
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
> fly p2 p1 100
> wait
> view p2
> display #1
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1740
> volume #1 region 0,0,0,2129,1523,1742
> volume #1 region 0,0,0,2129,1523,1743
> volume #1 region 0,0,0,2129,1523,1744
> volume #1 region 0,0,0,2129,1523,1743
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 13:49:38 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> display #2-5
> ~display #1
> display #1
> ~display #2-5
> volume all region 0,0,0,2129,1523,1743
> display #2-5
> view p2
> lighting soft
> view p1
> help hide
> hide #1
> view p2
> show #2
> volume #2-5 show style surface
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:08:40 2022 ———
opened ChimeraX session
> display #1
> ~display #2-5
> save /tmp/imprima/F107A3_bin2/F107-A3_session.cxs
——— End of log from Wed Jul 27 14:27:32 2022 ———
opened ChimeraX session
> view orient
> close session
> open /tmp/imprima/F107A1_bin2/data/f107a_flipz.mrc
Opened f107a_flipz.mrc as #1, grid size 1647,1506,1350, pixel 300, shown at
step 1, values int8
> save /tmp/imprima/F107A1_bin2/f107_A1_session.cxs
> volume showOutlineBox true
> volume #1 region 0,0,0,1646,1505,1349 step 8
> volume #1 region 0,0,0,1646,1505,1349 step 1 colorMode opaque8 imageMode
> "box faces"
> view orient
> view name p1
> view list
Named views: p1
> save /tmp/imprima/F107A1_bin2/f107_A1_session.cxs
> save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
> view name p2
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,1646,1505,1094
> view p1
> volume #1 region 0,0,0,1646,1505,1349
> volume #1 planes z,1349,1094
> wait 255
> wait
wait requires a frame count argument unless motion is in progress
> volume #1 region 0,0,0,1646,1505,1349
> volume #1 planes z,1349,1094
> wait 255
> volume #1 region 0,0,0,1646,1505,1349
> volume #1 planes z,1349,1300
> wait 50
> help 2dlabels
[Repeated 1 time(s)]
> volume #1 region 0,0,0,1646,1505,1349
> volume #1 planes z,1349,1300
> wait 50
> volume #1 region 0,0,0,1646,1505,1349
> 2dlabels arrow #7.1 start 0.083,0.643 end 0.357,0.413 color red weight 0.7
> headStyle solid
No 2D arrows in session
> 2dlabels arrow start 0.083,0.643 end 0.357,0.413 color red weight 0.7
> headStyle solid
> volume #1 region 0,0,0,1646,1505,1349
> view p1
> ui mousemode right "move label"
> 2dlabels arrow #2.1 end 0.363,0.765
> 2dlabels arrow #2.1 start 0.112,0.919
> 2dlabels arrow #2.1 start 0.112,0.919 end 0.363,0.765 color white
> 2dlabels arrow start 0.112,0.819 end 0.363,0.765 color white
> 2dlabels arrow #2.1 end 0.362,0.785
> 2dlabels arrow #2.2 end 0.343,0.523
> 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white
> help 2dlabels
> 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white bold false
Expected a keyword
> help 2dlabels
> 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 bold false color white
Expected ',' or a keyword
> 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white, bold
> false
Invalid "color" argument: Expected 'default' or a color
> view p1
> help 2dlabels
> 2dlabels arrow #2.2 start 0.112,0.819 end 0.343,0.523 color white weight 0.5
> 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
> margin 5 visibility true
> 2dlabels arrow #2.1 weight 0.5
> save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
> 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
> margin 5 visibility true
> 2dlabels arrow #2.1 end 0.362,0.784
> 2dlabels arrow #2.1 start 0.112,0.916
> 2dlabels arrow start 0.083,0.643 end 0.357,0.413 color red weight 0.5
> headStyle solid
> 2dlabels arrow #2.3 start 0.830,0.911
> 2dlabels arrow #2.3 end 0.580,0.728
> 2dlabels arrow #2.3 start 0.824,0.922
> 2dlabels arrow #2.3 start 0.824,0.922 end 0.580,0.728 color white
> save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
> 2dlabels arrow start 0.824,0.922 end 0.780,0.928 color white
> 2dlabels arrow #2.4 end 0.652,0.427
> 2dlabels arrow #2.3 start 0.813,0.939
> 2dlabels arrow #2.4 start 0.851,0.886
> 2dlabels arrow #2.4 weight 0.5
> 2dlabels arrow #2.4 weight 0.5 headStyle solid
> 2dlabels arrow #2.4 end 0.655,0.424
> save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
> volume #1 region 0,0,0,1646,1505,1349
[Repeated 1 time(s)]
> volume #1 region 0,0,0,1646,1505,1300
> 2dlabels arrow #2.1 end 0.442,0.807
> 2dlabels arrow #2.2 end 0.331,0.561
> 2dlabels arrow #2.3 end 0.591,0.756
> 2dlabels arrow #2.4 end 0.662,0.510
> volume #1 region 0,0,0,1646,1505,1349
> help 2dlabels\
No help found for '2dlabels\'
> help 2dlabels
> 2dlabels #all visbility false
Expected 'all' or a 2d label name or a label models specifier or a keyword
> 2dlabels all visbility false
Expected a keyword
> 2dlabels all visibility false
> 2dlabels arrow all visibility false
> save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
> volume #1 region 0,0,0,1646,1505,1300
> volume #1 region 0,0,0,1646,1300,1000 wait 100;
Expected a keyword
> volume #1 region 0,0,0,1646,1300,1000
> wait 100
> volume #1 region 0,0,0,1646,1505,1349
> volume #1 planes z,1349,1300
> wait 50
> volume #1 planes z,1300,1000
> wait 101
> save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
> volume #1 region 0,0,0,1646,1505,1349
> save /tmp/imprima/F107A1_bin2/f107_A1_session_fly.cxs
——— End of log from Fri Jul 29 13:26:07 2022 ———
opened ChimeraX session
> close #2
> close #3
> save /tmp/imprima/F107A1_bin2/f107_A1_session_fly_base.cxs
——— End of log from Fri Jul 29 15:52:14 2022 ———
opened ChimeraX session
> 2dlabels text Nuclei size 18 xpos .03 ypos .92 bold true bgColor black
> margin 5 visibility false
> 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
> visibility false
> 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
> visibility false
> 2dlabels text Mitochondria size 18 xpos .83 ypos .92 bold true bgColor black
> margin 5 visibility false
> 2dlabels arrow start 0.824,0.922 end 0.580,0.728 color white weight 0.5
> visibility false
> 2dlabels arrow start 0.851,0.886 end 0.662,0.510 color white weight 0.5
> visibility false
> 2dlabels text Microvilli size 18 xpos .03 ypos .42 bold true bgColor black
> margin 5 visibility false
> 2dlabels arrow start 0.112,0.916 end 0.442,0.807 color white weight 0.5
> visibility false
> 2dlabels arrow start 0.112,0.819 end 0.331,0.561 color white weight 0.5
> visibility false
> 2dlabels delete all
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/label/label2d.py", line 280, in label_delete
l.delete()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/label/arrows.py", line 414, in delete
lm.delete_arrow(self)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/label/arrows.py", line 312, in delete_arrow
del self._named_arrows[arrow.name]
KeyError: 'arrow 1'
KeyError: 'arrow 1'
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/label/arrows.py", line 312, in delete_arrow
del self._named_arrows[arrow.name]
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:5
Manufacturer: ASUSTeK COMPUTER INC.
Model: ESC4000A-E10
OS: AlmaLinux 8.5 Arctic Sphynx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 64 AMD EPYC 7513 32-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 251Gi 61Gi 9.4Gi 66Gi 180Gi 121Gi
Swap: 1.6Ti 885Mi 1.6Ti
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1)
Subsystem: ASUSTeK Computer Inc. Device [1043:87d5]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
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
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → KeyError deleting 2D arrow |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Eduardo,
--Eric