Opened 4 years ago

Last modified 4 years ago

#6182 feedback defect

'Combine' unexpectedly moving some atoms

Reported by: esa-pekka.kumpula@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-167-generic-x86_64-with-glibc2.27
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
I open a multi-chain model, and then split it to its chains using "split #1 chains". I then further split one of the chains into two different domains using "split atoms :1-100 atoms :100-200". I have a template structure that I want to superpose these two domains on, so I use matchmaker to align the two domains separately on the template. After this process, I want to combine the domains back into a single model using "combine #1.1.1-2". This does combine the models together, but the second domain in the list (#1.1.2) gets translated and rotated from the position I assigned to it using matchmaker. From the documentation I gather that this must be because the coordinate system of the first model is used for the comgination, but I don't understand why the second domain gets translated and rotated.

Log:
> alias views view initial sel; view sel orient; view name front; turn x 90;
> view name top; turn x 180; view name bottom; turn x 90; turn y 90; view name
> left; turn y 90; view name back; turn y 90; view name right; turn y 90

> color name tab01 #1f77b4

Color 'tab01' is opaque: rgb(12.2%, 46.7%, 70.6%) hex: #1f77b4

  

> color name tab02 #aec7e8

Color 'tab02' is opaque: rgb(68.2%, 78%, 91%) hex: #aec7e8

  

> color name tab03 #ff7f0e

Color 'tab03' is opaque: rgb(100%, 49.8%, 5.49%) hex: #ff7f0e

  

> color name tab04 #ffbb78

Color 'tab04' is opaque: rgb(100%, 73.3%, 47.1%) hex: #ffbb78

  

> color name tab05 #2ca02c

Color 'tab05' is opaque: rgb(17.3%, 62.7%, 17.3%) hex: #2ca02c

  

> color name tab06 #98df8a

Color 'tab06' is opaque: rgb(59.6%, 87.5%, 54.1%) hex: #98df8a

  

> color name tab07 #d62728

Color 'tab07' is opaque: rgb(83.9%, 15.3%, 15.7%) hex: #d62728

  

> color name tab08 #ff9896

Color 'tab08' is opaque: rgb(100%, 59.6%, 58.8%) hex: #ff9896

  

> color name tab09 #9467bd

Color 'tab09' is opaque: rgb(58%, 40.4%, 74.1%) hex: #9467bd

  

> color name tab10 #c5b0d5

Color 'tab10' is opaque: rgb(77.3%, 69%, 83.5%) hex: #c5b0d5

  

> color name tab11 #8c564b

Color 'tab11' is opaque: rgb(54.9%, 33.7%, 29.4%) hex: #8c564b

  

> color name tab12 #c49c94

Color 'tab12' is opaque: rgb(76.9%, 61.2%, 58%) hex: #c49c94

  

> color name tab13 #e377c2

Color 'tab13' is opaque: rgb(89%, 46.7%, 76.1%) hex: #e377c2

  

> color name tab14 #f7b6d2

Color 'tab14' is opaque: rgb(96.9%, 71.4%, 82.4%) hex: #f7b6d2

  

> color name tab15 #7f7f7f

Color 'tab15' is opaque: gray(49.8%) hex: #7f7f7f

  

> color name tab16 #c7c7c7

Color 'tab16' is opaque: gray(78%) hex: #c7c7c7

  

> color name tab17 #bcbd22

Color 'tab17' is opaque: rgb(73.7%, 74.1%, 13.3%) hex: #bcbd22

  

> color name tab18 #dbdb8d

Color 'tab18' is opaque: rgb(85.9%, 85.9%, 55.3%) hex: #dbdb8d

  

> color name tab19 #17becf

Color 'tab19' is opaque: rgb(9.02%, 74.5%, 81.2%) hex: #17becf

  

> color name tab20 #9edae5

Color 'tab20' is opaque: rgb(62%, 85.5%, 89.8%) hex: #9edae5

  

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> alias mask_gen volume threshold sel minimum $1 set 0 modelId 100; volume
> threshold #100 maximum $2 setMaximum 1; close #100

> graphics bgColor white

> graphics silhouettes true

> lighting soft

> alias strock stop; st; rock

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /data/data_epk/Commander_reprocess_aligned_volumes/cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus.mrc

Opened cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus.mrc as #1,
grid size 276,276,276, pixel 1.69, shown at level 0.0691, step 2, values
float32  

> open
> /data/data_epk/Commander_reprocess_aligned_volumes/cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus.mrc

Opened cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus.mrc as #2,
grid size 276,276,276, pixel 1.69, shown at level 0.0618, step 2, values
float32  

> open
> /data/data_epk/Commander_reprocess_aligned_volumes/cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus.mrc

Opened cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus.mrc as #3,
grid size 276,276,276, pixel 1.69, shown at level 0.072, step 2, values
float32  

> hide #!2 models

> hide #!3 models

> volume gaussian #1 sDev 3

Opened cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus.mrc
gaussian as #4, grid size 276,276,276, pixel 1.69, shown at step 1, values
float32  

> close #4

> volume gaussian #1 sDev 3

Opened cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus.mrc
gaussian as #4, grid size 276,276,276, pixel 1.69, shown at step 1, values
float32  

> volume gaussian #2 sDev 3

Opened cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus.mrc
gaussian as #5, grid size 276,276,276, pixel 1.69, shown at step 1, values
float32  

> volume gaussian #3 sDev 3

Opened cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus.mrc
gaussian as #6, grid size 276,276,276, pixel 1.69, shown at step 1, values
float32  

> ui tool show "Segment Map"

> hide #!5 models

> hide #!6 models

Segmenting cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus.mrc
gaussian, density threshold 0.076094  
Showing 18 region surfaces  
214 watershed regions, grouped to 18 regions  
Showing cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus
gaussian.seg - 18 regions, 18 surfaces  

> volume #4 level 0.003917

Segmenting cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus.mrc
gaussian, density threshold 0.003917  
Showing 18 region surfaces  
228 watershed regions, grouped to 18 regions  
Showing cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus
gaussian.seg - 18 regions, 18 surfaces  

> hide #!4 models

Deleted 13 regions  
Ungrouped to 2 regions  
[Repeated 1 time(s)]

> select clear

Ungrouped to 4 regions  
Grouped 4 regions  
Ungrouped to 0 regions  
Ungrouped to 4 regions  
Ungrouped to 2 regions  
Ungrouped to 0 regions  
Deleted 4 regions  
Deleted 1 regions  
Grouped 6 regions  
Saving 1 regions to mrc file...  
Opened
cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc
as #8, grid size 121,125,89, pixel 1.69, shown at step 1, values float32  
Wrote
cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc  
Segmenting cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus.mrc
gaussian, density threshold 0.056740  
Showing 17 region surfaces  
168 watershed regions, grouped to 17 regions  
Showing cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus
gaussian.seg - 17 regions, 17 surfaces  

> show #!5 models

> volume #5 level 0.005239

Segmenting cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus.mrc
gaussian, density threshold 0.005239  
Showing 17 region surfaces  
293 watershed regions, grouped to 17 regions  
Showing cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus
gaussian.seg - 17 regions, 17 surfaces  

> hide #!5 models

> show #!5 models

> hide #!5 models

Ungrouped to 2 regions  
Ungrouped to 10 regions  
Drag select of 401, 400, 394, 391, 94, 108, 85, 86, 100, 300, 129, 135, 340,
60  
Deleted 13 regions  
Segmenting cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus.mrc
gaussian, density threshold 0.005239  
Showing 17 region surfaces  
293 watershed regions, grouped to 17 regions  
Showing cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus
gaussian.seg - 17 regions, 17 surfaces  

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

Deleted 14 regions  
Ungrouped to 2 regions  
Ungrouped to 10 regions  
Deleted 4 regions  
Ungrouped to 2 regions  
Deleted 1 regions  
Ungrouped to 0 regions  
Grouped 7 regions  
Grouped 2 regions  

> select clear

Drag select of 408  
Saving 1 regions to mrc file...  
Opened
cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc
as #9, grid size 106,132,106, pixel 1.69, shown at step 1, values float32  
Wrote
cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc  

> hide #!9 models

> show #!9 models

> show #!6 models

> volume #6 level 0.004775

Segmenting cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus.mrc
gaussian, density threshold 0.004775  
Showing 22 region surfaces  
269 watershed regions, grouped to 22 regions  
Showing cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus
gaussian.seg - 22 regions, 22 surfaces  

> select clear

Drag select of 3, 2, 1, 6
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus.mrc gaussian  
[Repeated 1 time(s)]Deleted 3 regions  
Ungrouped to 6 regions  
Ungrouped to 8 regions  
Ungrouped to 2 regions  

> select clear

Deleted 1 regions  

> select #6

2 models selected  
Select one or more regions to delete  

> select clear

Deleted 1 regions  
Grouped 8 regions  
Grouped 3 regions  
Ungrouped to 2 regions  
Ungrouped to 3 regions  
Deleted 1 regions  
Grouped 3 regions  
Ungrouped to 3 regions  

> select clear

Deleted 1 regions  
Grouped 2 regions  
Ungrouped to 7 regions  

> select clear

Deleted 1 regions  
Ungrouped to 5 regions  
Deleted 1 regions  
Grouped 5 regions  
Grouped 2 regions  
Grouped 3 regions  
Ungrouped to 3 regions  
Ungrouped to 2 regions  
Deleted 1 regions  
Grouped 3 regions  
Ungrouped to 3 regions  
Grouped 2 regions  
Ungrouped to 6 regions  
Deleted 1 regions  
Grouped 8 regions  

> select clear

Grouped 2 regions  
Grouped 3 regions  
Deleted 6 regions  
Ungrouped to 2 regions  
Ungrouped to 5 regions  

> show #!8 models

> hide #!8 models

> show #!6 models

> hide #!6 models

Deleted 4 regions  
Ungrouped to 5 regions  
Deleted 2 regions  
[Repeated 1 time(s)]Ungrouped to 5 regions  
Deleted 1 regions  
[Repeated 1 time(s)]Ungrouped to 0 regions  
Deleted 3 regions  
Ungrouped to 2 regions  
[Repeated 1 time(s)]

> select clear

Ungrouped to 0 regions  
Grouped 5 regions  

> show #!6 models

> color #6 white models transparency 0

> hide #!6 models

Drag select of 362, 317, 368, 119, 375, 396, 6, 46, 397, 9
cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc  

> select clear

> hide #!9 models

> show #!6 models

> volume #6 level 0.06211

Deleted 1 regions  
Ungrouped to 3 regions  
Deleted 1 regions  
Grouped 2 regions  

> show #!3 models

> hide #!6 models

Drag select of 362, 317, 119, 375, 396, 46, 355, 398, 3
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus.mrc  

> select clear

> hide #!3 models

> show #!3 models

Deleted 1 regions  
[Repeated 1 time(s)]Ungrouped to 2 regions  
Ungrouped to 5 regions  
Deleted 1 regions  
Grouped 5 regions  

> hide #!3 models

Drag select of 362, 317, 375, 396, 279, 399  
Grouped 6 regions  
Saving 1 regions to mrc file...  
Opened
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_delete_some_more_manually.mrc
as #10, grid size 114,126,119, pixel 1.69, shown at step 1, values float32  
Wrote
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_delete_some_more_manually.mrc  

> show #!3 models

> hide #!3 models

> ui tool show "Map Eraser"

> volume #10 level 0.004529

> volume erase #10 center 218.9,251.7,212.1 radius 34.23

> select clear

> ui tool show "Map Eraser"

> volume erase #10 center 177.18,162.95,224.28 radius 33.856

> select #10

2 models selected  

> save /data/data_epk/Commander_reprocess_3_non-
> ring_masks/cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_manually_fixed.mrc
> models #10

> close #10

> open /data/data_epk/Commander_reprocess_3_non-
> ring_masks/cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_manually_fixed.mrc

Opened
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_manually_fixed.mrc
as #7, grid size 114,126,119, pixel 1.69,1.69,1.69, shown at level 0.182, step
1, values float32  

> volume #7 level 0.004733

> volume #9 level 0.003952

> show #!8 models

> volume #9 level 0.004868

> select #7

2 models selected  

> mask_gen 0.004 0.003

Opened
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_manually_fixed.mrc
thresholded as #100, grid size 114,126,119, pixel 1.69,1.69,1.69, shown at
step 1, values float32  
Opened
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_manually_fixed.mrc
thresholded as #10, grid size 114,126,119, pixel 1.69,1.69,1.69, shown at step
1, values float32  

> select #8

2 models selected  

> mask_gen 0.004 0.003

Opened
cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc
thresholded as #100, grid size 121,125,89, pixel 1.69, shown at step 1, values
float32  
Opened
cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc
thresholded as #11, grid size 121,125,89, pixel 1.69, shown at step 1, values
float32  

> select #9

2 models selected  

> mask_gen 0.004 0.003

Opened
cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc
thresholded as #100, grid size 106,132,106, pixel 1.69, shown at step 1,
values float32  
Opened
cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc
thresholded as #12, grid size 106,132,106, pixel 1.69, shown at step 1, values
float32  

> volume resample #10 onGrid #1

Opened
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_manually_fixed.mrc
thresholded resampled as #13, grid size 276,276,276, pixel 1.69, shown at step
1, values float32  

> close #13

> show #!10 models

> volume resample #10 onGrid #1

Opened
cryosparc_P1_J467_007_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate_manually_fixed.mrc
thresholded resampled as #13, grid size 276,276,276, pixel 1.69, shown at step
1, values float32  

> volume resample #11 onGrid #1

Opened
cryosparc_P1_J462_005_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc
thresholded resampled as #14, grid size 276,276,276, pixel 1.69, shown at step
1, values float32  

> volume resample #12 onGrid #1

Opened
cryosparc_P1_J463_004_volume_map_sharp_aligned_to_consensus_region_MASK_intermediate.mrc
thresholded resampled as #15, grid size 276,276,276, pixel 1.69, shown at step
1, values float32  

> save /data/data_epk/Commander_reprocess_3_non-
> ring_masks/cryosparc_P1_J467_007_MASK_final.mrc models #13

> save /data/data_epk/Commander_reprocess_3_non-
> ring_masks/cryosparc_P1_J462_005_MASK_final.mrc models #14

> save /data/data_epk/Commander_reprocess_3_non-
> ring_masks/cryosparc_P1_J463_004_MASK_final.mrc models #15

> open /home/epkumpu/Downloads/cryosparc_P1_J527_011_volume_map_sharp.mrc

Opened cryosparc_P1_J527_011_volume_map_sharp.mrc as #16, grid size
552,552,552, pixel 0.846, shown at level 0.0405, step 4, values float32  

> hide #!15 models

> hide #!14 models

> hide #!13 models

> ~select #9

Nothing selected  

> select #16

2 models selected  

> volume #16 level 0.114

> volume #16 step 1

> volume #16 level 0.1824

> volume #16 level 0.2508

> volume #16 level 0.2981

> open /home/epkumpu/Downloads/cryosparc_P1_J522_003_volume_map_sharp.mrc

Opened cryosparc_P1_J522_003_volume_map_sharp.mrc as #17, grid size
552,552,552, pixel 0.846, shown at level 0.0156, step 4, values float32  

> volume #17 level 0.03684

> volume #17 step 1

> volume #17 level 0.09225

> hide #!16 models

> volume #17 level 0.02706

> open /data/data_epk/Commander_reprocess_3_non-
> ring_masks/cryosparc_P1_J463_004_MASK_final.mrc

Opened cryosparc_P1_J463_004_MASK_final.mrc as #18, grid size 276,276,276,
pixel 1.69, shown at level 1, step 2, values float32  

> volume #18 level 0.08287

> open /home/epkumpu/Downloads/cryosparc_P1_J526_009_volume_map_sharp.mrc

Opened cryosparc_P1_J526_009_volume_map_sharp.mrc as #19, grid size
552,552,552, pixel 0.846, shown at level 0.0377, step 4, values float32  

> show #!16 models

> hide #!17 models

> hide #!18 models

> select clear

> volume #19 level 0.1535

> volume #19 step 1

> select #19

2 models selected  

> transparency sel 50

> select clear

Drag select of 16 cryosparc_P1_J527_011_volume_map_sharp.mrc , 19
cryosparc_P1_J526_009_volume_map_sharp.mrc  

> volume sel level 0.154

> open "/home/epkumpu/Downloads/cryosparc_P1_J483_007_volume_map_sharp
> (3).mrc"

Opened cryosparc_P1_J483_007_volume_map_sharp (3).mrc as #20, grid size
552,552,552, pixel 0.846, shown at level 0.0553, step 4, values float32  

> volume #20 level 0.09363

> volume #20 step 1

> volume #20 level 0.1711

> select clear

> hide #!19 models

> volume #20 level 0.154

> open /home/epkumpu/Downloads/cryosparc_P1_J531_mask.mrc

Opened cryosparc_P1_J531_mask.mrc as #21, grid size 552,552,552, pixel 0.846,
shown at level 1, step 4, values float32  

> volume #21 level 0.7993

> open /home/epkumpu/Downloads/cryosparc_P1_J533_mask.mrc

Opened cryosparc_P1_J533_mask.mrc as #22, grid size 552,552,552, pixel 0.846,
shown at level 1, step 4, values float32  

> volume #22 level 0.8361

> volume #22 level 0.8

> select #21

2 models selected  

> transparency sel 50

> select clear

> hide #!20 models

> show #!20 models

> hide #!21 models

> hide #!22 models

> open "/home/epkumpu/Downloads/cryosparc_P1_J488_mask (1).mrc"

Opened cryosparc_P1_J488_mask (1).mrc as #23, grid size 552,552,552, pixel
0.846, shown at level 0.504, step 4, values float32  

> select #23

2 models selected  

> transparency sel 50

> select clear

> volume #23 level 0.7254

> open /home/epkumpu/Downloads/cryosparc_P1_J536_mask.mrc

Opened cryosparc_P1_J536_mask.mrc as #24, grid size 552,552,552, pixel 0.846,
shown at level 0.754, step 4, values float32  

> select #24

2 models selected  

> transparency sel 50

> volume #24 level 0.1774

> volume #24 level 0.7238

> volume sel showOutlineBox true

> close session

> open
> /data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb

Summary of feedback from opening
/data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb  
---  
warning | Ignored bad PDB record found on line 31  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb #1  
---  
Chain | Description  
A | comm domain-containing protein 9  
B | comm domain-containing protein 10  
C | comm domain-containing protein 3  
D | comm domain-containing protein 5  
E | comm domain-containing protein 2  
F | comm domain-containing protein 1  
G | comm domain-containing protein 7  
H | comm domain-containing protein 4  
I | comm domain-containing protein 6  
J | comm domain-containing protein 8  
  

> open
> /data/data_epk/Commander_fits/flexible_fitting/cryosparc_P4_J86_006_volume_map_sharp.mrc

Opened cryosparc_P4_J86_006_volume_map_sharp.mrc as #2, grid size 568,568,568,
pixel 0.82, shown at level 0.0623, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.1458

> volume #2 level 0.4289

> select /D:123@CG2

1 atom, 1 residue, 1 model selected  

> select up

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

175 atoms, 175 bonds, 12 residues, 1 model selected  

> select up

3495 atoms, 3527 bonds, 224 residues, 1 model selected  

> select up

29810 atoms, 30060 bonds, 1875 residues, 1 model selected  

> hide

> show cartoons

> select clear

> open
> /data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb

Summary of feedback from opening
/data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb  
---  
warning | Ignored bad PDB record found on line 31  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb #3  
---  
Chain | Description  
A | comm domain-containing protein 9  
B | comm domain-containing protein 10  
C | comm domain-containing protein 3  
D | comm domain-containing protein 5  
E | comm domain-containing protein 2  
F | comm domain-containing protein 1  
G | comm domain-containing protein 7  
H | comm domain-containing protein 4  
I | comm domain-containing protein 6  
J | comm domain-containing protein 8  
  

> hide

> show cartoons

> mmaker #1/c to #3/g

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain G (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb, chain C
(#1), sequence alignment score = 261.5  
RMSD between 75 pruned atom pairs is 1.012 angstroms; (across all 188 pairs:
8.934)  
  

> hide #1 models

> select :lys

5154 atoms, 4930 bonds, 234 residues, 2 models selected  

> show sel

> color sel & #3 byhetero

> hide

> show #1 models

> mmaker #1/g to #3/c

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain C (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb, chain G
(#1), sequence alignment score = 261.5  
RMSD between 75 pruned atom pairs is 1.012 angstroms; (across all 188 pairs:
8.934)  
  

> hide #3 models

> select #3

29810 atoms, 30060 bonds, 1875 residues, 1 model selected  

> ~select #3

Nothing selected  

> select #2

2 models selected  

> transparency sel 50

> hide #1 models

> show #3 models

> open 6vac

6vac title:  
Mouse retromer (VPS26/VPS35/VPS29) heterotrimer [more info...]  
  
Chain information for 6vac #4  
---  
Chain | Description | UniProt  
A | Vacuolar protein sorting-associated protein 35 | VPS35_MOUSE  
B | Vacuolar protein sorting-associated protein 26A | VP26A_MOUSE  
C | Vacuolar protein sorting-associated protein 29 | VPS29_MOUSE  
  

> hide #!2 models

> hide #3 models

> view #4

Drag select of 1202 residues, 6 pseudobonds  

> color sel bychain

> select clear

Drag select of 1 residues  

> open "/data/data_epk/Commander_fits/Work/CComplex
> Fits/cryosparc_P1_J250_005_volume_map_sharp.mrc"

Opened cryosparc_P1_J250_005_volume_map_sharp.mrc as #5, grid size
276,276,276, pixel 1.69, shown at level 0.431, step 2, values float32  

> ui tool show "Side View"

> select #5

2 models selected  

> transparency sel 50

> select clear

[Repeated 1 time(s)]Drag select of 1202 residues, 6 pseudobonds  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,26.276,0,1,0,37.644,0,0,1,12.895

> view matrix models #4,1,0,0,53.867,0,1,0,103.67,0,0,1,42.299

> view matrix models
> #4,-0.24009,0.82372,0.51365,38.342,0.90282,-0.0049922,0.42999,74.352,0.35676,0.56697,-0.74247,130.54

> view matrix models
> #4,-0.3377,0.92596,0.16897,77.535,0.8145,0.37745,-0.4406,137.46,-0.47175,-0.011163,-0.88166,325.34

> view matrix models
> #4,-0.3377,0.92596,0.16897,94.101,0.8145,0.37745,-0.4406,182.54,-0.47175,-0.011163,-0.88166,315.88

> volume #5 level 1.192

> view matrix models
> #4,-0.085406,0.98801,0.12859,106.34,0.88965,0.13373,-0.43662,195.35,-0.44858,0.077106,-0.89041,314.12

> view matrix models
> #4,-0.29131,0.94295,0.16121,133.31,0.83367,0.33289,-0.44066,176.36,-0.46918,0.006023,-0.88308,325.1

> view matrix models
> #4,-0.30754,0.93731,0.1639,133.16,0.82726,0.34849,-0.44068,174.91,-0.47017,6.5342e-05,-0.88257,325.53

> view matrix models
> #4,-0.14995,0.91769,0.3679,92.258,0.97102,0.06664,0.22954,115.32,0.18613,0.39166,-0.90109,195.13

> view matrix models
> #4,-0.30377,0.93808,0.16651,133.57,0.83405,0.34631,-0.42945,165.06,-0.46052,0.0084211,-0.88761,345.57

> view matrix models
> #4,-0.30377,0.93808,0.16651,133.15,0.83405,0.34631,-0.42945,167.08,-0.46052,0.0084211,-0.88761,339.48

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.27273,0.5963,-0.75501,215.51,0.90404,-0.4273,-0.010915,210.99,-0.32913,-0.67959,-0.65562,386.51

> view matrix models
> #4,0.40337,0.51361,-0.75729,210.54,0.84213,-0.5321,0.087684,220.82,-0.35792,-0.67311,-0.64716,388.21

> view matrix models
> #4,0.50926,0.65177,-0.56201,156.27,0.7621,-0.038158,0.64633,99.863,0.39981,-0.75746,-0.51615,290.33

> ui tool show "Fit in Map"

Fit molecule 6vac (#4) to map cryosparc_P1_J250_005_volume_map_sharp.mrc (#5)
using 5957 atoms  
average map value = 0.6136, steps = 436  
shifted from previous position = 6.77  
rotated from previous position = 39.2 degrees  
atoms outside contour = 4590, contour level = 1.1923  
  
Position of 6vac (#4) relative to cryosparc_P1_J250_005_volume_map_sharp.mrc
(#5) coordinates:  
Matrix rotation and translation  
-0.13253070 0.77811374 -0.61398259 218.48722494  
0.93319902 0.30671019 0.18726572 97.81793298  
0.33402875 -0.54814950 -0.76678349 304.48915813  
Axis -0.60788239 -0.78361092 0.12819100  
Axis point 1.18307065 0.00000000 184.93058783  
Rotation angle (degrees) 142.77840619  
Shift along axis -170.43296780  
  

> view matrix models
> #4,-0.13253,0.77811,-0.61398,241.27,0.9332,0.30671,0.18727,95.202,0.33403,-0.54815,-0.76678,314.8

> view matrix models
> #4,0.31463,0.89118,-0.32683,137.35,0.77278,-0.040541,0.63338,108.18,0.5512,-0.45184,-0.70144,267.61

> view matrix models
> #4,0.37639,0.83125,-0.40909,147.3,0.75366,-0.017917,0.65702,104.77,0.53882,-0.55561,-0.63323,274.77

> view matrix models
> #4,0.37639,0.83125,-0.40909,162.47,0.75366,-0.017917,0.65702,94.016,0.53882,-0.55561,-0.63323,274.97

> view matrix models
> #4,0.55033,0.7995,-0.2407,125.34,0.63573,-0.21435,0.74155,124.48,0.54128,-0.56112,-0.62623,274.57

Fit molecule 6vac (#4) to map cryosparc_P1_J250_005_volume_map_sharp.mrc (#5)
using 5957 atoms  
average map value = 0.7687, steps = 148  
shifted from previous position = 19.3  
rotated from previous position = 19.5 degrees  
atoms outside contour = 4581, contour level = 1.1923  
  
Position of 6vac (#4) relative to cryosparc_P1_J250_005_volume_map_sharp.mrc
(#5) coordinates:  
Matrix rotation and translation  
0.69971668 0.66196084 -0.26870880 134.87717777  
0.66512968 -0.46631957 0.58322257 156.28045444  
0.26076633 -0.58681676 -0.76658138 317.84672033  
Axis -0.91105496 -0.41227755 0.00246743  
Axis point 0.00000000 111.12056517 143.27081422  
Rotation angle (degrees) 140.04884422  
Shift along axis -186.52718036  
  

> volume #5 step 1

> cofr sel

> select clear

> select #4/C:182

5 atoms, 4 bonds, 1 residue, 1 model selected  

> hide #!5 models

> select #4/C:2

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show #!5 models

Drag select of 1 residues  

> hide #!4 models

> hide #!5 models

> show #!2 models

> select #2

2 models selected  

> cofr centerOfView

> open "/home/epkumpu/Downloads/cryosparc_P1_J483_007_volume_map_sharp
> (3).mrc"

Opened cryosparc_P1_J483_007_volume_map_sharp (3).mrc as #6, grid size
552,552,552, pixel 0.846, shown at level 0.0553, step 4, values float32  

> volume #6 level 0.1675

> volume #6 step 1

> show #!2 models

> hide #!6 models

> volume #2 level 0.1966

> show #!5 models

> hide #!2 models

> show #1 models

> show #3 models

> show #!4 models

> close #5-6

> show #!2 models

> select clear

> hide #!4 models

> hide #1 models

> close #1

> open /data/data_epk/Commander_fits/flexible_fitting/commands_for_AF2.com

Install the SEQCROW bundle to open "Gaussian input file" format files.  
Opener for format 'Gaussian input file' is not installed; see log for more
info  

> open
> /data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb

Summary of feedback from opening
/data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb  
---  
warning | Ignored bad PDB record found on line 31  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb #1  
---  
Chain | Description  
A | comm domain-containing protein 9  
B | comm domain-containing protein 10  
C | comm domain-containing protein 3  
D | comm domain-containing protein 5  
E | comm domain-containing protein 2  
F | comm domain-containing protein 1  
G | comm domain-containing protein 7  
H | comm domain-containing protein 4  
I | comm domain-containing protein 6  
J | comm domain-containing protein 8  
  

> select #1/D:3@C

1 atom, 1 residue, 1 model selected  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

421 atoms, 428 bonds, 30 residues, 1 model selected  

> select clear

> hide sel

> hide

> hide #!2 models

> show #!2 models

> hide #!2 models

> select /g

6374 atoms, 6432 bonds, 400 residues, 2 models selected  

> select /c

7074 atoms, 7129 bonds, 2 pseudobonds, 569 residues, 4 models selected  

> mmaker

> matchmaker

Missing or invalid "matchAtoms" argument: empty atom specifier  

> split #1 chains

Split COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb (#1)
into 10 models  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb J #1.10  
---  
Chain | Description  
J | No description available  
  

> mmaker #1/c to #3/g:1-132

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain G (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C, chain C
(#1.3), sequence alignment score = 161.4  
RMSD between 76 pruned atom pairs is 1.017 angstroms; (across all 120 pairs:
3.014)  
  

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> show #1 cartoons

> mmaker #1/c to #3/g:132-300

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain G (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C, chain C
(#1.3), sequence alignment score = 105.9  
RMSD between 56 pruned atom pairs is 0.902 angstroms; (across all 69 pairs:
2.423)  
  

> mmaker #1/g to #3/c:132-300

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain C (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G, chain G
(#1.7), sequence alignment score = 83  
RMSD between 43 pruned atom pairs is 0.858 angstroms; (across all 60 pairs:
4.419)  
  

> combine

Remapping chain ID 'A' in 6vac #4 to 'K'  
Remapping chain ID 'B' in 6vac #4 to 'L'  
Remapping chain ID 'C' in 6vac #4 to 'M'  
Remapping chain ID 'A' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb A #1.1 to
'N'  
Remapping chain ID 'B' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb B #1.2 to
'O'  
Remapping chain ID 'C' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C #1.3 to
'P'  
Remapping chain ID 'D' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb D #1.4 to
'Q'  
Remapping chain ID 'E' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb E #1.5 to
'R'  
Remapping chain ID 'F' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb F #1.6 to
'S'  
Remapping chain ID 'G' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G #1.7 to
'T'  
Remapping chain ID 'H' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb H #1.8 to
'U'  
Remapping chain ID 'I' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb I #1.9 to
'V'  
Remapping chain ID 'J' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb J #1.10 to
'W'  

> close #5

> combine #1 modelId #1

Traceback (most recent call last):  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/atomic/cmd.py", line 64, in combine_cmd  
session.models.add([combination])  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 654, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 721, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
ValueError: Tried to add model combination #1 with the same id as another
model COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb #1  
  
ValueError: Tried to add model combination #1 with the same id as another
model COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb #1  
  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 721, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
  
See log for complete Python traceback.  
  

> combine #1.1-10 modelId #1

Traceback (most recent call last):  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/atomic/cmd.py", line 64, in combine_cmd  
session.models.add([combination])  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 654, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 721, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
ValueError: Tried to add model combination #1 with the same id as another
model COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb #1  
  
ValueError: Tried to add model combination #1 with the same id as another
model COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb #1  
  
File "/cs/group/grp-cryoem/apps/chimerax/chimerax/lib/python3.9/site-
packages/chimerax/core/models.py", line 721, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
  
See log for complete Python traceback.  
  

> combine #1.1-10

> hide #!1 models

> show #!1 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #3 models

> hide #!1 models

> hide #5 models

> show #5 models

> show #3 models

> hide #5 models

> show #5 models

> hide #3 models

> show #3 models

> hide #3 models

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #5 models

> show #5 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #3 models

> hide #5 models

> show #5 models

> hide #3 models

> hide #5 models

> show #5 models

> show #!1 models

> hide #1.1 models

> hide #1.2 models

> hide #1.3 models

> hide #1.4 models

> hide #1.5 models

> hide #1.6 models

> hide #1.7 models

> hide #1.8 models

> hide #1.9 models

> hide #1.10 models

> hide #5 models

> show #5 models

> close #5

> show #1.1 models

> show #1.2 models

> hide #1.2 models

> hide #1.1 models

> show #1.1 models

> show #1.2 models

> select clear

> show #1.3 models

> show #1.4 models

> show #1.5 models

> show #1.6 models

> show #1.7 models

> show #1.8 models

> show #1.9 models

> show #1.10 models

> show #!2 models

> hide #!2 models

> show #3 models

> hide #3 models

> show #3 models

> rename #1.1 id #2

> rename #1.1 id #10

> rename #2.2 id #10

> rename #10 id #1.1

> hide #1.3 models

> show #1.3 models

> combine #1

> hide #!1 models

> hide #3 models

> hide #1.1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #5 models

> show #5 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #5 models

> close #5

> save
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainC_swapped_to_G.pdb
> models #1.3 relModel #2

> save
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainG_swapped_to_C.pdb
> relModel #2

> save
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainG_swapped_to_C.pdb
> models #1.7 relModel #2

> open
> /data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes14_ISOLDE_roughly_correct_chainswap_C_and_G.pdb

Summary of feedback from opening
/data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes14_ISOLDE_roughly_correct_chainswap_C_and_G.pdb  
---  
warnings | Ignored bad PDB record found on line 31  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
6277 messages similar to the above omitted  
  
Chain information for
COMMD_fixed_clashes14_ISOLDE_roughly_correct_chainswap_C_and_G.pdb #5  
---  
Chain | Description  
A | comm domain-containing protein 9  
B | comm domain-containing protein 10  
C | comm domain-containing protein 3  
D | comm domain-containing protein 5  
E | comm domain-containing protein 2  
F | comm domain-containing protein 1  
G | comm domain-containing protein 7  
H | comm domain-containing protein 4  
I | comm domain-containing protein 6  
J | comm domain-containing protein 8  
  

> hide #5

> show #5 cartoons

> select clear

> close #5

> close #1

> open
> /data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb

Summary of feedback from opening
/data/data_epk/Commander_fits/flexible_fitting/Steps/COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb  
---  
warning | Ignored bad PDB record found on line 31  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb #1  
---  
Chain | Description  
A | comm domain-containing protein 9  
B | comm domain-containing protein 10  
C | comm domain-containing protein 3  
D | comm domain-containing protein 5  
E | comm domain-containing protein 2  
F | comm domain-containing protein 1  
G | comm domain-containing protein 7  
H | comm domain-containing protein 4  
I | comm domain-containing protein 6  
J | comm domain-containing protein 8  
  

> hide #1

> show #1 cartoons

> save /data/data_epk/Commander_blender/COMMD_Ring.obj

> show #3 models

> hide #1 models

> hide #3 models

> show #3 models

> show #1 models

> split #1 chains

Split COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb (#1)
into 10 models  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb J #1.10  
---  
Chain | Description  
J | No description available  
  

> hide #1.2 models

> hide #1.1 models

> hide #1.4 models

> hide #1.5 models

> hide #1.6 models

> hide #1.8 models

> hide #1.9 models

> hide #1.10 models

> mmaker #1.3 to #3/g:132-300

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain G (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C, chain C
(#1.3), sequence alignment score = 105.9  
RMSD between 56 pruned atom pairs is 0.902 angstroms; (across all 69 pairs:
2.423)  
  

> mmaker #1.7 to #3/c:132-300

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain C (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G, chain G
(#1.7), sequence alignment score = 83  
RMSD between 43 pruned atom pairs is 0.858 angstroms; (across all 60 pairs:
4.419)  
  

> hide #3 models

> split #1.7 atoms :1-131 atoms :132-400

Split COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G
(#1.7) into 2 models  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G 1 #1.7.1  
---  
Chain | Description  
G | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G 2 #1.7.2  
---  
Chain | Description  
G | No description available  
  

> split #1.3 atoms :1-118 atoms :119-400

Split COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C
(#1.3) into 2 models  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C 1 #1.3.1  
---  
Chain | Description  
C | No description available  
  
Chain information for
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C 2 #1.3.2  
---  
Chain | Description  
C | No description available  
  

> show #3 models

> select #3

29810 atoms, 30060 bonds, 1875 residues, 1 model selected  

> transparency 50 sel

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

> transparency sel 50

> select clear

> select #3

29810 atoms, 30060 bonds, 1875 residues, 1 model selected  

> transparency sel 90

> transparency sel 90 target r

> transparency sel 50 target r

> select clear

> select #3

29810 atoms, 30060 bonds, 1875 residues, 1 model selected  

> transparency sel 90 target r

> select clear

> select #1.3.1/C:116

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

398 atoms, 399 bonds, 24 residues, 1 model selected  

> select up

1851 atoms, 1867 bonds, 118 residues, 1 model selected  

> hide #1.3.1 models

> show #1.3.1 models

> select clear

> mmaker #1.3.1 to #3/g:1-128

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain G (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C 1, chain
C (#1.3.1), sequence alignment score = 158.9  
RMSD between 75 pruned atom pairs is 1.012 angstroms; (across all 115 pairs:
2.925)  
  

> mmaker #1.7.1 to #3/c:1-121

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb,
chain C (#3) with
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G 1, chain
G (#1.7.1), sequence alignment score = 162.8  
RMSD between 75 pruned atom pairs is 1.012 angstroms; (across all 116 pairs:
3.086)  
  

> select clear

> help help:user

> combine #1.3.1-2 modelId #10

Remapping chain ID 'C' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C 2 #1.3.2
to 'D'  

> close #10

> combine #1.3.1-2 modelId #10 name chainC

Remapping chain ID 'C' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C 2 #1.3.2
to 'D'  

> combine #1.7.1-2 modelId #11 name chainG

Remapping chain ID 'G' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb G 2 #1.7.2
to 'H'  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #3 models

> save
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainC_swapped_to_G.pdb
> models #10 relModel #2

> open
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainC_swapped_to_G.pdb

Chain information for ChainC_swapped_to_G.pdb #5  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> hide #10 models

> show #10 models

> save
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainG_swapped_to_C.pdb
> models #11 relModel #2

> open
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainG_swapped_to_C.pdb

Chain information for ChainG_swapped_to_C.pdb #6  
---  
Chain | Description  
G | No description available  
H | No description available  
  

> close #10-11

> show #3 models

> close #5

> show #!1 models

> open
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainC_swapped_to_G.pdb

Chain information for ChainC_swapped_to_G.pdb #5  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> help help:user

> combine #1.3.1-2 modelId #10 name chainC

Remapping chain ID 'C' in
COMMD_fixed_clashes13_ISOLDE_roughly_correct_chains_ABCDEFGHIJ.pdb C 2 #1.3.2
to 'D'  

> hide #5 models

> close #5-6,10

> save
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainC_swapped_to_G_Nt.pdb
> models #1.3.1 relModel #2

> save
> /data/data_epk/Commander_fits/flexible_fitting/Steps/ChainC_swapped_to_G_Ct.pdb
> models #1.3.2 relModel #2




OpenGL version: 3.3.0 NVIDIA 470.103.01
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 30BAS0PF00
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Xeon(R) Silver 4108 CPU @ 1.80GHz
Cache Size: 11264 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        7.4G         92G        205M         25G        116G
	Swap:          126G          0B        126G

Graphics:
	65:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)	
	Subsystem: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    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-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → 'Combine' unexpectedly moving some atoms

comment:2 by Eric Pettersen, 4 years ago

Status: accepted → feedback

Hi Esa-Pekka,

I tried and failed to reproduce this. Could you save a session just before the problematic "combine" command and send it to me? If it's large you could send it directly to me (pett@…). It would also be fine to delete/close chains and structures that aren't relevant to the problem, which would also cut down on the size. Thanks!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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