perframe / clip front problem

[jacquero@…]

The following bug report has been submitted:
Platform:        macOS-13.6.5-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Clipping is not dependable. I cannot always run the command "clip front x"
and I am trying to record a movie using "perframe "clip front $1" range x,y" which is not really working at all.

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> surface cap mesh false

Opened cryosparc_P266_J489_class_00_00012_volume.mrc z flip as #4, grid size
320,320,320, pixel 2.32, shown at level 0.189, step 1, values float32  
Log from Thu Mar 28 15:41:05 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> surface cap mesh false

Opened cryosparc_P266_J489_class_00_00012_volume.mrc z flip as #4, grid size
320,320,320, pixel 2.32, shown at level 0.189, step 1, values float32  
Log from Thu Mar 28 12:36:15 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> surface cap mesh false

Opened cryosparc_P266_J489_class_00_00012_volume.mrc z flip as #4, grid size
320,320,320, pixel 2.32, shown at level 0.189, step 1, values float32  
Log from Thu Mar 28 11:53:11 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> surface cap mesh false

Opened cryosparc_P266_J489_class_00_00012_volume.mrc z flip as #4, grid size
320,320,320, pixel 2.32, shown at level 0.189, step 1, values float32  
Log from Wed Mar 27 17:10:25 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> surface cap mesh false

Log from Wed Mar 27 13:42:28 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> surface cap mesh false

Log from Tue Oct 3 14:48:44 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7muc

Summary of feedback from opening 7muc fetched from pdb  
---  
note | Fetching compressed mmCIF 7muc from
http://files.rcsb.org/download/7muc.cif  
  
7muc title:  
Legionella pneumophila Dot/Icm T4SS C1 Reconstruction [more info...]  
  
Chain information for 7muc #1  
---  
Chain | Description | UniProt  
AC BC CC DC EC FC GC HC IC JC KC LC MC | DotC | O52184_LEGPN 1-303  
AD Ad BD Bd CD Cd DD Dd ED Ed FD Fd GD Gd HD Hd ID Id JD Jd KD Kd LD Ld MD Md
| DotD | O52183_LEGPN 1-163  
AF Af BF Bf CF Cf DF Df EF Ef FF Ff GF Gf HF Hf IF If JF Jf KF Kf LF Lf MF Mf
VF WF XF YF ZF | DotF | O54615_LEGPN 1-269  
AG BG CG DG EG FG GG HG IG JG KG LG MG VG WG XG YG ZG | IcmE protein |
O53087_LEGPN 1-1048  
AH BH CH DH EH FH GH HH IH JH KH LH MH VH WH XH YH ZH | Type IV secretion
protein IcmK | A0A2S6FBG9_LEGPN 1-361  
AK BK CK DK EK FK GK HK IK JK KK LK MK | Inner membrane lipoprotein YiaD |
O53086_LEGPN 1-189  
AL BL CL DL EL FL GL HL IL JL KL LL ML | Outer membrane protein, OmpA family
protein | Q5ZXS4_LEGPH 1-249  
AM BM CM DM EM FM GM HM IM JM KM LM MM | DUF2807 domain-containing protein |
A0A2S6F0F8_LEGPN 1-320  
AN BN CN DN EN FN GN HN IN JN KN LN MN | Neurogenic locus notch |
A0A2S6FAR3_LEGPN 1-124  
AU BU CU DU EU FU GU HU IU JU KU LU MU | Unknown protein fragment |  
AX BX CX DX EX FX GX HX IX JX KX LX MX VX WX XX YX ZX | Unknown protein
fragment |  
  

> sequence chain
> #1/AC#1/BC#1/CC#1/DC#1/EC#1/FC#1/GC#1/HC#1/IC#1/JC#1/KC#1/LC#1/MC

Alignment identifier is 1  

> select /AC/BC/CC/DC/EC/FC/GC/HC/IC/JC/KC/LC/MC

21905 atoms, 22321 bonds, 26 pseudobonds, 2769 residues, 2 models selected  

> ui tool show "Color Actions"

> color (#!1 & sel) #ffffffff

> open 7muq

7muq title:  
Reconstruction of the Legionella pneumophila Dot/Icm T4SS 3DVA Map 1 [more
info...]  
  
Chain information for 7muq #2  
---  
Chain | Description | UniProt  
AC BC CC DC EC FC GC HC IC JC KC LC MC | DotC | O52184_LEGPN 0-302 1-303 2-304  
AD Ad BD Bd CD Cd DD Dd ED Ed FD Fd GD Gd HD Hd ID Id JD Jd KD Kd LD Ld MD Md
| DotD | O52183_LEGPN 1-163  
AF Af BF Bf CF Cf DF Df EF Ef FF Ff GF Gf HF Hf IF If JF Jf KF Kf LF Lf MF Mf
VF WF XF YF ZF | DotF | O54615_LEGPN 1-269  
AG Ag BG Bg CG Cg DG Dg EG Eg FG Fg GG Gg HG Hg IG Ig JG Jg KG Kg LG Lg MG Mg
NG OG PG VG WG XG YG ZG | IcmE protein | O53087_LEGPN 1-1048  
AH BH CH DH EH FH GH HH IH JH KH LH MH VH WH XH YH ZH | Type IV secretion
protein IcmK | A0A2S6FBG9_LEGPN 1-361  
AK BK CK DK EK FK GK HK IK JK KK LK MK | Inner membrane lipoprotein YiaD |
O53086_LEGPN 1-189  
AL BL CL DL EL FL GL HL IL JL KL LL ML | Outer membrane protein, OmpA family
protein | Q5ZXS4_LEGPH 1-249  
AM BM CM DM EM FM GM HM IM JM KM LM MM | DUF2807 domain-containing protein |
A0A2S6F0F8_LEGPN 1-320  
AN BN CN DN EN FN GN HN IN JN KN LN MN | Neurogenic locus notch |
A0A2S6FAR3_LEGPN 1-124  
AU BU CU DU EU FU GU HU IU JU KU LU MU | Unknown protein fragment |  
AX BX CX DX EX FX GX HX IX JX KX LX MX VX WX XX YX ZX | Unknown protein
fragment |  
  

> color (#!1 & sel) #b02419ff

> color (#!1 & sel) #7d401bff

> select
> #1/AC#1/BC#1/CC#1/DC#1/EC#1/FC#1/GC#1/HC#1/IC#1/JC#1/KC#1/LC#1/MC#2/AC#2/BC#2/CC#2/DC#2/EC#2/FC#2/GC#2/HC#2/IC#2/JC#2/KC#2/LC#2/MC

44846 atoms, 45722 bonds, 26 pseudobonds, 5656 residues, 3 models selected  

> color (#!1-2 & sel) #7c3e19ff

> color (#!1-2 & sel) #7b3f1bff

> color (#!1-2 & sel) #7b411bff

> select
> #1/AD#1/Ad#1/BD#1/Bd#1/CD#1/Cd#1/DD#1/Dd#1/ED#1/Ed#1/FD#1/Fd#1/GD#1/Gd#1/HD#1/Hd#1/ID#1/Id#1/JD#1/Jd#1/KD#1/Kd#1/LD#1/Ld#1/MD#1/Md#2/AD#2/Ad#2/BD#2/Bd#2/CD#2/Cd#2/DD#2/Dd#2/ED#2/Ed#2/FD#2/Fd#2/GD#2/Gd#2/HD#2/Hd#2/ID#2/Id#2/JD#2/Jd#2/KD#2/Kd#2/LD#2/Ld#2/MD#2/Md

55744 atoms, 56810 bonds, 7202 residues, 2 models selected  

> color sel #b02419ff

[Repeated 1 time(s)]

> select
> #1/AD#1/Ad#1/BD#1/Bd#1/CD#1/Cd#1/DD#1/Dd#1/ED#1/Ed#1/FD#1/Fd#1/GD#1/Gd#1/HD#1/Hd#1/ID#1/Id#1/JD#1/Jd#1/KD#1/Kd#1/LD#1/Ld#1/MD#1/Md#2/AD#2/Ad#2/BD#2/Bd#2/CD#2/Cd#2/DD#2/Dd#2/ED#2/Ed#2/FD#2/Fd#2/GD#2/Gd#2/HD#2/Hd#2/ID#2/Id#2/JD#2/Jd#2/KD#2/Kd#2/LD#2/Ld#2/MD#2/Md

55744 atoms, 56810 bonds, 7202 residues, 2 models selected  

> select ~sel

317006 atoms, 322983 bonds, 78 pseudobonds, 41374 residues, 4 models selected  

> hide sel atoms

> select ~sel

55744 atoms, 56810 bonds, 7202 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select add #2

220242 atoms, 224415 bonds, 34 pseudobonds, 28722 residues, 3 models selected  

> select subtract #2

27872 atoms, 28405 bonds, 3601 residues, 1 model selected  

> select add #1

180380 atoms, 183783 bonds, 44 pseudobonds, 23455 residues, 2 models selected  

> show sel cartoons

> hide #!2 models

> select
> #1/AC#1/BC#1/CC#1/DC#1/EC#1/FC#1/GC#1/HC#1/IC#1/JC#1/KC#1/LC#1/MC#2/AC#2/BC#2/CC#2/DC#2/EC#2/FC#2/GC#2/HC#2/IC#2/JC#2/KC#2/LC#2/MC

44846 atoms, 45722 bonds, 26 pseudobonds, 5656 residues, 3 models selected  

> show sel & #!1 cartoons

> show #!2 models

> select add #2

214275 atoms, 218331 bonds, 60 pseudobonds, 27890 residues, 4 models selected  

> select add #1

372750 atoms, 379793 bonds, 78 pseudobonds, 48576 residues, 4 models selected  

> show sel cartoons

> select clear

> select
> #1/AG#1/BG#1/CG#1/DG#1/EG#1/FG#1/GG#1/HG#1/IG#1/JG#1/KG#1/LG#1/MG#1/VG#1/WG#1/XG#1/YG#1/ZG#2/AG#2/Ag#2/BG#2/Bg#2/CG#2/Cg#2/DG#2/Dg#2/EG#2/Eg#2/FG#2/Fg#2/GG#2/Gg#2/HG#2/Hg#2/IG#2/Ig#2/JG#2/Jg#2/KG#2/Kg#2/LG#2/Lg#2/MG#2/Mg#2/NG#2/OG#2/PG#2/VG#2/WG#2/XG#2/YG#2/ZG

29600 atoms, 30008 bonds, 16 pseudobonds, 3864 residues, 3 models selected  

> select ~sel

343150 atoms, 349785 bonds, 62 pseudobonds, 44712 residues, 4 models selected  

> hide sel cartoons

> select add #2

367782 atoms, 374789 bonds, 78 pseudobonds, 47964 residues, 4 models selected  

> select subtract #2

175412 atoms, 178779 bonds, 44 pseudobonds, 22843 residues, 2 models selected  

> select add #1

180380 atoms, 183783 bonds, 44 pseudobonds, 23455 residues, 2 models selected  

> show sel cartoons

> select clear

> select #1/AG,BG,CG,DG,EG,FG,GG,HG,IG, JG, KG, LG, MG

3588 atoms, 3614 bonds, 442 residues, 1 model selected  

> select #1/AD,BD,CD,DD,ED,FD,GD,HD,ID, JD, KD, LD, MD

14118 atoms, 14391 bonds, 1820 residues, 1 model selected  

> select #1/AdMD

Nothing selected  

> select #1/Ad

1058 atoms, 1078 bonds, 137 residues, 1 model selected  

> select #1/Ad, Bd, Cd, Dd, Ed, Fd, Gd, Hd, Id, Jd, Kd, Ld, Md

13754 atoms, 14014 bonds, 1781 residues, 1 model selected  

> color sel #9d5e55ff

> select
> #1/AL#1/BL#1/CL#1/DL#1/EL#1/FL#1/GL#1/HL#1/IL#1/JL#1/KL#1/LL#1/ML#2/AL#2/BL#2/CL#2/DL#2/EL#2/FL#2/GL#2/HL#2/IL#2/JL#2/KL#2/LL#2/ML

36088 atoms, 36842 bonds, 26 pseudobonds, 4498 residues, 4 models selected  

> color (#!1-2 & sel) #09215dff

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select
> #1/AM#1/BM#1/CM#1/DM#1/EM#1/FM#1/GM#1/HM#1/IM#1/JM#1/KM#1/LM#1/MM#2/AM#2/BM#2/CM#2/DM#2/EM#2/FM#2/GM#2/HM#2/IM#2/JM#2/KM#2/LM#2/MM

51610 atoms, 52481 bonds, 6500 residues, 2 models selected  

> color sel #e6caa1ff

> select
> #1/AH#1/BH#1/CH#1/DH#1/EH#1/FH#1/GH#1/HH#1/IH#1/JH#1/KH#1/LH#1/MH#1/VH#1/WH#1/XH#1/YH#1/ZH#2/AH#2/BH#2/CH#2/DH#2/EH#2/FH#2/GH#2/HH#2/IH#2/JH#2/KH#2/LH#2/MH#2/VH#2/WH#2/XH#2/YH#2/ZH

70308 atoms, 72068 bonds, 10 pseudobonds, 9138 residues, 4 models selected  

> color (#!1-2 & sel) #dda438ff

> select
> #1/AK#1/BK#1/CK#1/DK#1/EK#1/FK#1/GK#1/HK#1/IK#1/JK#1/KK#1/LK#1/MK#2/AK#2/BK#2/CK#2/DK#2/EK#2/FK#2/GK#2/HK#2/IK#2/JK#2/KK#2/LK#2/MK

30550 atoms, 31070 bonds, 3926 residues, 2 models selected  

> color sel #67c5eeff

> select
> #1/AF#1/Af#1/BF#1/Bf#1/CF#1/Cf#1/DF#1/Df#1/EF#1/Ef#1/FF#1/Ff#1/GF#1/Gf#1/HF#1/Hf#1/IF#1/If#1/JF#1/Jf#1/KF#1/Kf#1/LF#1/Lf#1/MF#1/Mf#1/VF#1/WF#1/XF#1/YF#1/ZF#2/AF#2/Af#2/BF#2/Bf#2/CF#2/Cf#2/DF#2/Df#2/EF#2/Ef#2/FF#2/Ff#2/GF#2/Gf#2/HF#2/Hf#2/IF#2/If#2/JF#2/Jf#2/KF#2/Kf#2/LF#2/Lf#2/MF#2/Mf#2/VF#2/WF#2/XF#2/YF#2/ZF

29062 atoms, 29496 bonds, 3802 residues, 2 models selected  

> color sel #69389bff

> select
> #1/AN#1/BN#1/CN#1/DN#1/EN#1/FN#1/GN#1/HN#1/IN#1/JN#1/KN#1/LN#1/MN#2/AN#2/BN#2/CN#2/DN#2/EN#2/FN#2/GN#2/HN#2/IN#2/JN#2/KN#2/LN#2/MN

15132 atoms, 15548 bonds, 2028 residues, 2 models selected  

> color sel #3b541fff

> lighting simple

> select clear

> lighting soft

> lighting full

> lighting simple

> lighting gentle

> lighting flat

> lighting flat intensity 2

> lighting flat intensity 1.2

> lighting gentle intensity 1.2

> lighting soft intensity 1.2

> cd /Users/jacquelynroberts/Desktop/dis_paper/newfig1

Current working directory is:
/Users/jacquelynroberts/Desktop/dis_paper/newfig1  

> view orient

> save top.png supersample 3

> ui tool show "Side View"

> view orient

[Repeated 2 time(s)]

> show atoms

> save side.png supersample 3

> ui mousemode right "rotate selected models"

> hide atoms

> save sidemodel.png supersample 3

> save sidemodel.png supersample 3 transparency 100

Expected a keyword  

> save sidemodel.png supersample 3 transparency t

Expected a keyword  

> save /Users/jacquelynroberts/Desktop/dis_paper/newfig1/realcolors.cxs

——— End of log from Tue Oct 3 14:48:44 2023 ———

opened ChimeraX session  

> select
> #1/AG#1/BG#1/CG#1/DG#1/EG#1/FG#1/GG#1/HG#1/IG#1/JG#1/KG#1/LG#1/MG#1/VG#1/WG#1/XG#1/YG#1/ZG#2/AG#2/Ag#2/BG#2/Bg#2/CG#2/Cg#2/DG#2/Dg#2/EG#2/Eg#2/FG#2/Fg#2/GG#2/Gg#2/HG#2/Hg#2/IG#2/Ig#2/JG#2/Jg#2/KG#2/Kg#2/LG#2/Lg#2/MG#2/Mg#2/NG#2/OG#2/PG#2/VG#2/WG#2/XG#2/YG#2/ZG

29600 atoms, 30008 bonds, 16 pseudobonds, 3864 residues, 3 models selected  

> show sel atoms

> hide sel cartoons

[Repeated 1 time(s)]

> select ~sel

343150 atoms, 349785 bonds, 62 pseudobonds, 44712 residues, 4 models selected  

> hide sel cartoons

> hide #!2 models

> show #!2 models

> select add #2

367782 atoms, 374789 bonds, 78 pseudobonds, 47964 residues, 4 models selected  

> select subtract #2

175412 atoms, 178779 bonds, 44 pseudobonds, 22843 residues, 2 models selected  

> select add #1

180380 atoms, 183783 bonds, 44 pseudobonds, 23455 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> show sel atoms

> clip off

> select clear

> lighting soft

> perframe "clip front $1" ranges 0,10

> clip off

> perframe "clip front $1" ranges 20,30

> clip off

> ui mousemode right clip

> view orient

> turn y 90

> turn x 90

[Repeated 1 time(s)]

> clip off

> clip front 20

> clip off

> save /Users/jacquero/Desktop/dis_paper/newfig1/realcolors.cxs

——— End of log from Wed Mar 27 13:42:28 2024 ———

opened ChimeraX session  

> clip front -13

> clip off

> clip front 0

> view orient

> clip off

> view orient

> turn y 90

> turn x 180

> clip front -13

> clip front -20

> -18

Unknown command: -18  

> clip front -18

> clip front -15

> clip front -20

> clip front -10

> clip off

> clip front -10

> clip front -15

> clip off

> clip front -15

> clip off

> clip front -20

> clip off

> clip front -25

> clip front -30

> clip front -20

> clip off

> ui mousemode right clip

> select
> #1/AG#1/BG#1/CG#1/DG#1/EG#1/FG#1/GG#1/HG#1/IG#1/JG#1/KG#1/LG#1/MG#1/VG#1/WG#1/XG#1/YG#1/ZG#2/AG#2/Ag#2/BG#2/Bg#2/CG#2/Cg#2/DG#2/Dg#2/EG#2/Eg#2/FG#2/Fg#2/GG#2/Gg#2/HG#2/Hg#2/IG#2/Ig#2/JG#2/Jg#2/KG#2/Kg#2/LG#2/Lg#2/MG#2/Mg#2/NG#2/OG#2/PG#2/VG#2/WG#2/XG#2/YG#2/ZG

29600 atoms, 30008 bonds, 16 pseudobonds, 3864 residues, 3 models selected  

> select clear

> clip 0

Expected a keyword  

> clip back 14

> clip off

> clip front 0

> clip off

> clip front -20

> clip off

> clip front -25

> clip off

> clip front -35

> clip off

> clip front -40

> clip off

> clip front -25

> clip off

> clip front -20

> clip front 10

> clip front 25

> clip front 35

> clip off

> clip front -25

> clip front 35

> clip off

> clip front -25

> clip front -15

> clip off

> clip front -25

> clip front 15

> clip front 10

[Repeated 5 time(s)]

> clip off

> clip front -25

> clip front 10

[Repeated 10 time(s)]

> clip off

> clip front 10

> clip off

> clip front -40

> clip front 10

[Repeated 1 time(s)]

> clip off

> clip front -40

> clip front 10

[Repeated 10 time(s)]

> clip off

> hide #!2 models

> show #!2 models

> open /Users/jacquero/Downloads/cryosparc_P266_J489_class_00_00012_volume.mrc
> format mrc

Opened cryosparc_P266_J489_class_00_00012_volume.mrc as #3, grid size
320,320,320, pixel 2.32, shown at level 0.189, step 2, values float32  

> ui mousemode right "translate selected models"

> select add #3

2 models selected  

> view matrix models #3,1,0,0,-136.99,0,1,0,-91.402,0,0,1,-76.992

> view matrix models #3,1,0,0,-90.279,0,1,0,-86.873,0,0,1,-81.389

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.99924,0.023104,0.031396,-110.23,-0.031805,0.94889,0.31399,-173.8,-0.022537,-0.31475,0.94891,61.737

> volume flip #3

Opened cryosparc_P266_J489_class_00_00012_volume.mrc z flip as #4, grid size
320,320,320, pixel 2.32, shown at step 1, values float32  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.99924,0.023104,0.031396,-110.23,-0.031805,0.94889,0.31399,-173.8,-0.022537,-0.31475,0.94891,61.737

> hide #!2 models

> fitmap #1 inMap #4

Fit molecule 7muc (#1) to map cryosparc_P266_J489_class_00_00012_volume.mrc z
flip (#4) using 180380 atoms  
average map value = 0.2184, steps = 120  
shifted from previous position = 9.85  
rotated from previous position = 10.4 degrees  
atoms outside contour = 63102, contour level = 0.18878  
  
Position of 7muc (#1) relative to
cryosparc_P266_J489_class_00_00012_volume.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.99995410 0.00863372 -0.00415412 97.12039806  
-0.00914105 0.98958224 -0.14367820 134.79591690  
0.00287037 0.14370958 0.98961574 49.32293160  
Axis 0.99779591 -0.02438868 -0.06171313  
Axis point 0.00000000 -311.57317141 976.14537367  
Rotation angle (degrees) 8.28003040  
Shift along axis 90.57496885  
  

> color zone #4 near #1 distance 13.9

> hide #!1 models

> volume #4 color #942192

> volume #4 color darkgrey

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.  

> show #!2 models

> color zone #4 near #2 distance 13.9

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #4 color #a9a9a986

> volume #4 color #a9a9a987

> fitmap #2 inMap #4

Fit molecule 7muq (#2) to map cryosparc_P266_J489_class_00_00012_volume.mrc z
flip (#4) using 192370 atoms  
average map value = 0.22, steps = 116  
shifted from previous position = 10.7  
rotated from previous position = 9.27 degrees  
atoms outside contour = 65176, contour level = 0.18878  
  
Position of 7muq (#2) relative to
cryosparc_P266_J489_class_00_00012_volume.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.99997573 -0.00529421 -0.00452753 101.80792971  
0.00449782 0.98699104 -0.16071234 135.20287944  
0.00531948 0.16068807 0.98699090 44.97885898  
Axis 0.99906785 -0.03060928 0.03043836  
Axis point 0.00000000 -190.29069655 875.52056942  
Rotation angle (degrees) 9.25624494  
Shift along axis 98.94364932  
  

> color zone #4 near #2 distance 13.9

> show #!1 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.  

> hide #!2 models

> color zone #4 near #1 distance 13.9

> show #!2 models

> hide #!4 models

> save /Users/jacquero/Desktop/7mucplucdotgdome.pdb displayedOnly true

> open /Users/jacquero/Desktop/7mucplucdotgdome.pdb

Summary of feedback from opening /Users/jacquero/Desktop/7mucplucdotgdome.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 SERAC 30
GLNAC 35 1 6  
Start residue of secondary structure not found: HELIX 2 2 ALAAC 58 LYSAC 85 1
28  
Start residue of secondary structure not found: HELIX 3 3 GLNAC 86 TYRAC 94 1
9  
Start residue of secondary structure not found: HELIX 4 4 PHEAC 96 VALAC 100 1
5  
Start residue of secondary structure not found: HELIX 5 5 TRPAC 147 TRPAC 152
1 6  
3743 messages similar to the above omitted  
  
Chain information for 7mucplucdotgdome.pdb  
---  
Chain | Description  
5.1/AC 5.1/BC 5.1/CC 5.1/DC 5.1/EC 5.1/FC 5.1/GC 5.1/HC 5.1/IC 5.1/JC 5.1/KC
5.1/LC 5.1/MC | No description available  
5.1/AD 5.1/Ad 5.1/BD 5.1/Bd 5.1/CD 5.1/Cd 5.1/DD 5.1/Dd 5.1/ED 5.1/Ed 5.1/FD
5.1/Fd 5.1/GD 5.1/Gd 5.1/HD 5.1/Hd 5.1/ID 5.1/Id 5.1/JD 5.1/Jd 5.1/KD 5.1/Kd
5.1/LD 5.1/Ld 5.1/MD 5.1/Md | No description available  
5.1/AF 5.1/Af 5.1/BF 5.1/Bf 5.1/CF 5.1/Cf 5.1/DF 5.1/Df 5.1/EF 5.1/Ef 5.1/FF
5.1/Ff 5.1/GF 5.1/Gf 5.1/HF 5.1/Hf 5.1/IF 5.1/If 5.1/JF 5.1/Jf 5.1/KF 5.1/Kf
5.1/LF 5.1/Lf 5.1/MF 5.1/Mf 5.1/VF 5.1/WF 5.1/XF 5.1/YF 5.1/ZF | No
description available  
5.1/AG 5.1/BG 5.1/CG 5.1/DG 5.1/EG 5.1/FG 5.1/GG 5.1/HG 5.1/IG 5.1/JG 5.1/KG
5.1/LG 5.1/MG 5.1/VG 5.1/WG 5.1/XG 5.1/YG 5.1/ZG | No description available  
5.2/AG 5.2/BG 5.2/CG 5.2/DG 5.2/EG 5.2/FG 5.2/GG 5.2/HG 5.2/IG 5.2/JG 5.2/KG
5.2/LG 5.2/MG 5.2/NG 5.2/OG 5.2/PG | No description available  
5.1/AH 5.1/BH 5.1/CH 5.1/DH 5.1/EH 5.1/FH 5.1/GH 5.1/HH 5.1/IH 5.1/JH 5.1/KH
5.1/LH 5.1/MH 5.1/VH 5.1/WH 5.1/XH 5.1/YH 5.1/ZH | No description available  
5.1/AK 5.1/BK 5.1/CK 5.1/DK 5.1/EK 5.1/FK 5.1/GK 5.1/HK 5.1/IK 5.1/JK 5.1/KK
5.1/LK 5.1/MK | No description available  
5.1/AL 5.1/BL 5.1/CL 5.1/DL 5.1/EL 5.1/FL 5.1/GL 5.1/HL 5.1/IL 5.1/JL 5.1/KL
5.1/LL 5.1/ML | No description available  
5.1/AM 5.1/BM 5.1/CM 5.1/DM 5.1/EM 5.1/FM 5.1/GM 5.1/HM 5.1/IM 5.1/JM 5.1/KM
5.1/LM 5.1/MM | No description available  
5.1/AN 5.1/BN 5.1/CN 5.1/DN 5.1/EN 5.1/FN 5.1/GN 5.1/HN 5.1/IN 5.1/JN 5.1/KN
5.1/LN 5.1/MN | No description available  
5.1/AU 5.1/BU 5.1/CU 5.1/DU 5.1/EU 5.1/FU 5.1/GU 5.1/HU 5.1/IU 5.1/JU 5.1/KU
5.1/LU 5.1/MU | No description available  
5.1/AX 5.1/BX 5.1/CX 5.1/DX 5.1/EX 5.1/FX 5.1/GX 5.1/HX 5.1/IX 5.1/JX 5.1/KX
5.1/LX 5.1/MX 5.1/VX 5.1/WX 5.1/XX 5.1/YX 5.1/ZX | No description available  
5.2/Ag 5.2/Bg 5.2/Cg 5.2/Dg 5.2/Eg 5.2/Fg 5.2/Gg 5.2/Hg 5.2/Ig 5.2/Jg 5.2/Kg
5.2/Lg 5.2/Mg 5.2/VG 5.2/WG 5.2/XG 5.2/YG 5.2/ZG | No description available  
  

> hide #!1 models

> hide #!2 models

> close #5

> show #!4 models

> ui mousemode right clip

> open
> /Users/jacquero/Documents/icmX_pentamer/RebuildModel_9/refined_composite.pdb
> format pdb

Summary of feedback from opening
/Users/jacquero/Documents/icmX_pentamer/RebuildModel_9/refined_composite.pdb  
---  
warning | Ignored bad PDB record found on line 34999  
  
Chain information for refined_composite.pdb #5  
---  
Chain | Description  
A | No description available  
B C D E | No description available  
  

> view orient

[Repeated 1 time(s)]

> hide #!4 models

> hide #5 models

> show #5 models

> show #5 atoms

> view orient

[Repeated 1 time(s)]

> close #5

> show #!4 models

> clip off

> open
> /Users/jacquero/Documents/icmX_pentamer/RebuildModel_9/refined_composite.pdb
> format pdb

Summary of feedback from opening
/Users/jacquero/Documents/icmX_pentamer/RebuildModel_9/refined_composite.pdb  
---  
warning | Ignored bad PDB record found on line 34999  
  
Chain information for refined_composite.pdb #5  
---  
Chain | Description  
A | No description available  
B C D E | No description available  
  

> ui mousemode right "translate selected models"

> select add #5

34894 atoms, 35259 bonds, 2303 residues, 3 models selected  

> view matrix models
> #3,0.99924,0.023104,0.031396,-287.61,-0.031805,0.94889,0.31399,-221.41,-0.022537,-0.31475,0.94891,51.67,#5,1,0,0,-177.38,0,1,0,-47.613,0,0,1,-10.067

> view matrix models
> #3,0.99924,0.023104,0.031396,-318.28,-0.031805,0.94889,0.31399,-228.92,-0.022537,-0.31475,0.94891,49.32,#5,1,0,0,-208.05,0,1,0,-55.12,0,0,1,-12.417

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.70338,0.27835,0.65404,-599.97,-0.52315,0.82565,0.21123,113.19,-0.48121,-0.49074,0.72637,458.89,#5,0.72981,0.44712,0.51716,-473.74,-0.49705,0.86641,-0.047643,211.93,-0.46938,-0.22228,0.85456,315.76

> view matrix models
> #3,-0.027993,0.30056,0.95335,-407.66,-0.81962,0.53906,-0.19402,584.85,-0.57223,-0.78681,0.23126,880.85,#5,0.0089035,0.58544,0.81067,-354.98,-0.81263,0.47666,-0.3353,598.82,-0.58271,-0.65579,0.47999,673.01

> view matrix models
> #3,-0.012138,-0.38261,0.92383,-99.93,-0.86614,0.46568,0.18148,451.51,-0.49965,-0.79797,-0.33705,1135.4,#5,0.0080353,-0.072595,0.99733,-173.23,-0.84903,0.52642,0.045158,446.63,-0.52829,-0.84712,-0.057405,933.46

> view matrix models
> #3,-0.1518,-0.4356,0.88725,8.9083,-0.82457,0.55078,0.12934,420.18,-0.54502,-0.71196,-0.44279,1172.3,#5,-0.13389,-0.12993,0.98244,-89.085,-0.80716,0.58947,-0.032044,435.63,-0.57496,-0.79727,-0.18379,981.72

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.1518,-0.4356,0.88725,0.78837,-0.82457,0.55078,0.12934,367.86,-0.54502,-0.71196,-0.44279,1043.6,#5,-0.13389,-0.12993,0.98244,-97.205,-0.80716,0.58947,-0.032044,383.31,-0.57496,-0.79727,-0.18379,853.03

> view matrix models
> #3,-0.1518,-0.4356,0.88725,3.496,-0.82457,0.55078,0.12934,372.14,-0.54502,-0.71196,-0.44279,1083.5,#5,-0.13389,-0.12993,0.98244,-94.498,-0.80716,0.58947,-0.032044,387.59,-0.57496,-0.79727,-0.18379,892.87

> view matrix models
> #3,-0.1518,-0.4356,0.88725,3.762,-0.82457,0.55078,0.12934,362.46,-0.54502,-0.71196,-0.44279,1072.1,#5,-0.13389,-0.12993,0.98244,-94.232,-0.80716,0.58947,-0.032044,377.91,-0.57496,-0.79727,-0.18379,881.51

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.15828,-0.45937,0.87403,23.954,-0.78136,0.59946,0.17356,298.11,-0.60368,-0.65546,-0.45381,1081,#5,-0.14133,-0.15642,0.97753,-79.161,-0.76147,0.64817,-0.0063762,327.21,-0.63261,-0.74526,-0.21072,894.74

> view matrix models
> #3,-0.062391,-0.47855,0.87584,-14.653,-0.79301,0.55661,0.24764,285.47,-0.60601,-0.6791,-0.41422,1072.7,#5,-0.045902,-0.1771,0.98312,-111.19,-0.77177,0.63114,0.077663,305.3,-0.63424,-0.75518,-0.16565,881.75

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.062391,-0.47855,0.87584,-10.979,-0.79301,0.55661,0.24764,308.32,-0.60601,-0.6791,-0.41422,1076.8,#5,-0.045902,-0.1771,0.98312,-107.52,-0.77177,0.63114,0.077663,328.14,-0.63424,-0.75518,-0.16565,885.85

> view matrix models
> #3,-0.062391,-0.47855,0.87584,-14.172,-0.79301,0.55661,0.24764,287.47,-0.60601,-0.6791,-0.41422,1075.5,#5,-0.045902,-0.1771,0.98312,-110.71,-0.77177,0.63114,0.077663,307.29,-0.63424,-0.75518,-0.16565,884.53

> view matrix models
> #3,-0.062391,-0.47855,0.87584,-12.99,-0.79301,0.55661,0.24764,294.65,-0.60601,-0.6791,-0.41422,1077.2,#5,-0.045902,-0.1771,0.98312,-109.53,-0.77177,0.63114,0.077663,314.47,-0.63424,-0.75518,-0.16565,886.23

> ui mousemode right clip

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.062391,-0.47855,0.87584,55.664,-0.79301,0.55661,0.24764,282.99,-0.60601,-0.6791,-0.41422,1087.8,#5,-0.045902,-0.1771,0.98312,-40.872,-0.77177,0.63114,0.077663,302.82,-0.63424,-0.75518,-0.16565,896.83

> select #5:1-20

1296 atoms, 1300 bonds, 80 residues, 1 model selected  

> hide sel atoms

> select add #5

34894 atoms, 35259 bonds, 2303 residues, 1 model selected  

> view matrix models
> #5,-0.045902,-0.1771,0.98312,-33.198,-0.77177,0.63114,0.077663,307.93,-0.63424,-0.75518,-0.16565,896.69

> fitmap #5 inMap #4

Fit molecule refined_composite.pdb (#5) to map
cryosparc_P266_J489_class_00_00012_volume.mrc z flip (#4) using 34894 atoms  
average map value = 0.1862, steps = 240  
shifted from previous position = 15.8  
rotated from previous position = 12.9 degrees  
atoms outside contour = 16459, contour level = 0.18878  
  
Position of refined_composite.pdb (#5) relative to
cryosparc_P266_J489_class_00_00012_volume.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.00245617 0.00827946 0.99996271 -26.75281736  
-0.42698472 0.90423593 -0.00643808 185.86458301  
-0.90425551 -0.42695299 0.00575616 883.70466986  
Axis -0.21045920 0.95302270 -0.21784092  
Axis point 449.84231098 0.00000000 477.55865654  
Rotation angle (degrees) 92.50897466  
Shift along axis -9.74349381  
  

> color zone #4 near sel & #5 distance 13.9

> select add #1

215274 atoms, 219042 bonds, 44 pseudobonds, 25758 residues, 3 models selected  

> select add #2

407644 atoms, 415052 bonds, 78 pseudobonds, 50879 residues, 5 models selected  

> color zone #4 near sel distance 8

> select clear

> color #5 #0096ffff

> color #5 #76d6ffff

> color #5 #7a81ffff

> select add #5

34894 atoms, 35259 bonds, 2303 residues, 1 model selected  

> select add #1

215274 atoms, 219042 bonds, 44 pseudobonds, 25758 residues, 3 models selected  

> select add #2

407644 atoms, 415052 bonds, 78 pseudobonds, 50879 residues, 5 models selected  

> color zone #4 near sel distance 8

> select clear

> hide #5 models

> ui mousemode right clip

> view orient

> turn y 90

[Repeated 3 time(s)]

> view orient

> turn y 90

> turn x 90

> ui mousemode right zoom

> turn x 90

> turn x -10 9

[Repeated 3 time(s)]

> ui mousemode right clip

> turn x -10 9

> clip off

> view orient

> clip off

> turn x 90

> turn y 90

> turn x 90

[Repeated 1 time(s)]

> ui mousemode right zoom

> ui mousemode right clip

> turn x -10 9

[Repeated 4 time(s)]

> close #3

> save /Users/jacquero/Desktop/movie.cxs

——— End of log from Wed Mar 27 17:10:25 2024 ———

opened ChimeraX session  

> view orient

> turn y 90

> turn x 90

[Repeated 1 time(s)]

> ui mousemode right zoom

> turn x 90

[Repeated 2 time(s)]

> ui mousemode right clip

> select #4

2 models selected  
Drag select of 4 cryosparc_P266_J489_class_00_00012_volume.mrc z flip  

> select clear

> clip off

> ui mousemode right clip

> turn x 90

[Repeated 7 time(s)]

> turn x -10 9

> clip off

> view orient

> ui mousemode right zoom

> ui mousemode right clip

> turn y 90

> turn x -10 9

[Repeated 6 time(s)]

> view orient

> turn y 90

[Repeated 3 time(s)]

> turn x -10 9

> turn y 90

> clip off

> ui mousemode right zoom

> ui mousemode right clip

> view orient

[Repeated 2 time(s)]

> ui mousemode right zoom

> turn y 90

> turn x -10 9

[Repeated 2 time(s)]

> ui mousemode right clip

> turn x -10 9

[Repeated 3 time(s)]

> clip off

> turn x -10 9

[Repeated 7 time(s)]

> clip off

> cilp front 0

Unknown command: cilp front 0  

> cilp front

Unknown command: cilp front  

> view orient

> turn y 90

> turn x -10 9

[Repeated 1 time(s)]

> ui mousemode right zoom

> turn x -10 9

[Repeated 3 time(s)]

> view orient

[Repeated 2 time(s)]

> turn y 90

> turn x -10 9

[Repeated 2 time(s)]

> ui mousemode right clip

> turn x -10 9

[Repeated 3 time(s)]

> view orient

[Repeated 1 time(s)]

> clip off

> turn y 90

> turn x -10 9

[Repeated 1 time(s)]

> ui mousemode right zoom

> surface dust #4 size 23.2

> turn x -10 9

> ui mousemode right clip

> view orient

> turn y 90

> turn x -10 9

[Repeated 1 time(s)]

> ui mousemode right zoom

> turn x -10 9

[Repeated 5 time(s)]

> ui mousemode right clip

> hide #!4 models

> show #5 models

> show #!1 models

> view orient

> show #!2 models

> turn y 90

> turn x 90

[Repeated 1 time(s)]

> view name p1

> zoom 1.5

[Repeated 1 time(s)]

> hide #2

> turn x -90

> zoom 0.75

> move x -90

> move x 90

> move y -90

> move y 90

[Repeated 1 time(s)]

> p1

Unknown command: p1  

> view p1

> fly p1 p2

fly: Unknown position name "p2"  

> zoom 2

> view name p2

> view p1

> fly p1 p2

> hide #!2 models

> show #!2 models

> select
> #1/AG#1/BG#1/CG#1/DG#1/EG#1/FG#1/GG#1/HG#1/IG#1/JG#1/KG#1/LG#1/MG#1/VG#1/WG#1/XG#1/YG#1/ZG#2/AG#2/Ag#2/BG#2/Bg#2/CG#2/Cg#2/DG#2/Dg#2/EG#2/Eg#2/FG#2/Fg#2/GG#2/Gg#2/HG#2/Hg#2/IG#2/Ig#2/JG#2/Jg#2/KG#2/Kg#2/LG#2/Lg#2/MG#2/Mg#2/NG#2/OG#2/PG#2/VG#2/WG#2/XG#2/YG#2/ZG

29600 atoms, 30008 bonds, 16 pseudobonds, 3864 residues, 3 models selected  

> show sel atoms

> select clear

> crossfade hide
> #1/AG#1/BG#1/CG#1/DG#1/EG#1/FG#1/GG#1/HG#1/IG#1/JG#1/KG#1/LG#1/MG#1/VG#1/WG#1/XG#1/YG#1/ZG#2/AG#2/Ag#2/BG#2/Bg#2/CG#2/Cg#2/DG#2/Dg#2/EG#2/Eg#2/FG#2/Fg#2/GG#2/Gg#2/HG#2/Hg#2/IG#2/Ig#2/JG#2/Jg#2/KG#2/Kg#2/LG#2/Lg#2/MG#2/Mg#2/NG#2/OG#2/PG#2/VG#2/WG#2/XG#2/YG#2/ZG

Expected an integer >= 1 or a keyword  

> crossfade hide #1

Expected an integer >= 1 or a keyword  

> crossfade

> hide #1

> crossfade

> hide ~#1

> crossfade

> show #5

> select #5:1-20

1296 atoms, 1300 bonds, 80 residues, 1 model selected  

> delete #5:1-20

> view p2

> crossfade

> show #1

> crossfade

> show
> #1/AG#1/BG#1/CG#1/DG#1/EG#1/FG#1/GG#1/HG#1/IG#1/JG#1/KG#1/LG#1/MG#1/VG#1/WG#1/XG#1/YG#1/

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> crossfade

> show #1/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,VG,WG,XG,YG

> crossfade

> show atoms #1/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,VG,WG,XG,YG

Expected ',' or a keyword  

> crossfade

> show atoms #1/AG-YG

Expected ',' or a keyword  

> crossfade

> show #1/AG-YG

> select #2/JG

1229 atoms, 1250 bonds, 1 pseudobond, 165 residues, 2 models selected  

> show sel cartoons

> undo

> crossfade

> show #2/AG-YG

> select clear

> view p1

> turn x 90\

Expected a number or a keyword  

> turn x 90

[Repeated 2 time(s)]

> view name p3

> zoom 2

> zoom 1.8

> view p3

> zoom 1.8

> view name p4

> fly p4 p2

> hide #!1 models

> show #!1 models

> hide ~#1/AG-YG

> show #!4 models

> hide #!4 models

> roll z 3 120

> roll y 3 120

> view p2

> ui mousemode right "mark plane"

> ui mousemode right "mark surface"

> ui mousemode right "mark center"

> ui mousemode right "mark point"

> select #5/A:426@HE1

1 atom, 1 residue, 1 model selected  

> select #5/A:443@CE

1 atom, 1 residue, 1 model selected  

> ui mousemode right "mark plane"

> ui mousemode right "mark point"

> ui mousemode right "mark center"

> select #5/A:426@HE1

1 atom, 1 residue, 1 model selected  

> select #5/A:443@HE1

1 atom, 1 residue, 1 model selected  

> getcrd sel

Atom #5/A:443@HE1 235.335 279.889 287.493  

> marker #6 235.335 279.889 287.493

Expected a keyword  

> marker #5 235.335 279.889 287.493

Expected a keyword  

> marker #5 position 235.335 279.889 287.493

Invalid "position" argument: Expected 3 floats or object specifier  

> marker #5 position 235.335, 279.889, 287.493

Cannot create a marker set #5 with same model id as another model  

> marker #6 position 235.335, 279.889, 287.493

> save /Users/jacquero/Desktop/movie.cxs

——— End of log from Thu Mar 28 11:53:11 2024 ———

opened ChimeraX session  

> view p3

> turn x 90

[Repeated 2 time(s)]

> zoom 1.2

[Repeated 1 time(s)]

> view name p5

> select clear

> view p1

> movie record

> fly p1 p2 40

> fly p2 40 p1

> movie reset

> movie record

> fly p1 40 p2

> crossfade

> hide #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG

> wait 60

> crossfade

> show #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG

> fly p2 40 p1

> fly p1 60 p3 20 p4

> crossfade

> hide ~#5

> crossfade

> show #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG #1

> fly p3 20 p4 20 p5

> wait 25

> movie encode

Movie saved to /Users/jacquero/Desktop/movie.mp4  
  

> view p1

> movie record

> fly p1 40 p2

> crossfade

> hide #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG

> wait 60

> crossfade

> show #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG

> fly p2 40 p1

> fly p1 60 p3 20 p4

> crossfade

> hide ~#5

> roll y 3 120 center #6

> crossfade

> show #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG #1

> fly p4 20 p5

> movie encode movie2.mp4

Movie saved to movie2.mp4  
  

> view p1

> show #!4 models

> hide #!4 models

> crossfade

> show #4

> view p4

> crossfade

> hide ~#5

> color #4 silver models

> color #4 #c0c0c077 models

> perframe "clip #4 front $1" ranges -40, 0

Error executing per-frame command 'clip #4 front -40': Expected a keyword  

> perframe "clip front $1" ranges -40, 0

> clip off

> clip front 30

> clip front 20

> clip front 50

> clip off

> clip front 0

> show #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG #1

> view p1

> hide #!4 models

> movie record

> fly p1 40 p2

> crossfade

> hide #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG

> wait 60

> crossfade

> show #2/AG,BG,CG,DG,EG,FG,GG,HG,IG,JG,KG,LG,MG,NG,OG,PG

> fly p2 40 p1

> fly p1 60 p3 20 p4

> crossfade

> show #4

> clip front 0

[Repeated 1 time(s)]

> ui mousemode right clip

> movie reset

> clip front 0

> view p1

> hide #!4 models

> save /Users/jacquero/Desktop/movie.cxs

——— End of log from Thu Mar 28 12:36:15 2024 ———

opened ChimeraX session  

> show #!4 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 1 maps.  

> hide #!2 models

> hide #5 models

> color zone #4 near #1 distance 13.9

> color zone #4 near #1,#2,#5 distance 13.9

Invalid "near" argument: only initial part "#1" of atom specifier valid  

> color zone #4 near #1 #2 #5 distance 13.9

> show #5 models

> hide #5 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> view p3

> clip front 0

> ui mousemode right clip

> save /Users/jacquero/Desktop/movie.cxs

——— End of log from Thu Mar 28 15:41:05 2024 ———

opened ChimeraX session  

> view p3

> perframe "clip front $1" ranges -100,0

> clip off

> clip front 0

> clip off

> clip front -80

> clip off

> view p1

> movie record

> fly p1 20 p3 perframe "clip front $1" range -100,0

fly: Unknown position name "perframe"  

> movie record

Already recording a movie  

> fly p1 20 p3

> perframe "clip front $1" ranges -100,0

> clip front 0

> clip off

> clip front 0

> clip off

> perframe "clip front $1" ranges -100,0

> movie encode

Movie saved to /Users/jacquero/Desktop/movie.mp4  
  

> perframe "clip front $2" ranges -100,0

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/perframe.py", line 105, in _perframe_callback  
alias(session, *args, echo_tag=tag, log=False)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3463, in __call__  
text = self.expand(*args, optional=optional)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3445, in expand  
raise UserError("Not enough arguments")  
chimerax.core.errors.UserError: Not enough arguments  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/perframe.py", line 65, in cb  
_perframe_callback(data, session)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/perframe.py", line 108, in _perframe_callback  
if alias.cmd is not None:  
^^^^^^^^^  
AttributeError: 'Alias' object has no attribute 'cmd'  
  
Error processing trigger "new frame":  
AttributeError: 'Alias' object has no attribute 'cmd'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/perframe.py", line 108, in _perframe_callback  
if alias.cmd is not None:  
^^^^^^^^^  
  
See log for complete Python traceback.  
  

> perframe "clip front $1" ranges -100,0




OpenGL version: 4.1 INTEL-20.7.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.

Python: 3.11.2
Locale: 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: MacBook Pro
      Model Identifier: MacBookPro14,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 526.0.0.0.0
      OS Loader Version: 577.140.2~22
      SMC Version (system): 2.44f6

Software:

    System Software Overview:

      System Version: macOS 13.6.5 (22G621)
      Kernel Version: Darwin 22.6.0
      Time since boot: 6 days, 19 hours, 46 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 650:

      Chipset Model: Intel Iris Plus Graphics 650
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5927
      Revision ID: 0x0006
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        C24F390:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: HCHM800711  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 0.00


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Reported by Jacquelyn Roberts

[Tom Goddard]

I guess what you mean is that the clip plane is not positioned where you expect it to be. When you use the command

perframe "clip front $1" ranges -100,0

the first step "clip front -100" positions the plane 100 Angstroms in front of the center of the scene then the second step "clip front -99" moves the plane toward the viewer 99 Angstroms, then the third step moves it toward the viewer 98 Angstroms.... I suspect that is not what you want. This behavior is described in the clip command documentation

​https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clip.html

"The offsets are relative to the position reference point, if given. Otherwise, offsets are relative to the current positions of the planes, or (if a plane is newly activated) the center of the bounding box of displayed models."

You probably either want to specify the clip command "position" option to say what the offsets are relative to, or you could have a single "clip front -100" command then a 'perframe "clip front 1" range 100' to gradually move that plane 1 Angstrom away per frame.