Opened 2 years ago

Closed 2 years ago

#9327 closed defect (fixed)

unitcell issues

Reported by: dobromirak@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Higher-Order Structure Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Hello, I  am trying to visualize multiple unit cells and I am using the plugin Unit Cell. The file I input is a .pdb file with the crystallographic information and for example VMD reads it corectly. I think ChimeraX also reads it since the file appears in the "Atomic structure" menu of the plugin window. However, no matter the input in fields "Number of cells" and "offset" (for example 3 3 3, 1 1 1, respectivelly) only a single cell is displayed. I tried pressing enter after inputing the numbers, I tried clicking on make copies. I even tried the example in the manual, which was to input 3 1 1 and -1 0 0 and nothing worked - I always get a single unit cell displayed, not multiple ones.

Regards,
Dobromir

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF 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 E:/Downloads/IE/hpc/me_si/mtd_C-Si_ELT_1423K/traj_imgs/0.xyz

Unrecognized file suffix '.xyz'  

> help help:quickstart

> open E:/Downloads/IE/hpc/me_si/mtd_C-Si_ELT_1423K/traj_imgs/0.mol2

Opened 0.mol2 containing 1 structures (65 atoms, 81 bonds)  

> open "E:/Downloads/IE/hpc/me_si/mtd_C-Si_ELT_1423K/traj_imgs/eye
> length/1155.mol2"

Opened 1155.mol2 containing 1 structures (65 atoms, 74 bonds)  

> close #1

> show atoms

> hide atoms

> show atoms

> show cartoons

> hide cartoons

> style ball

Changed 65 atom styles  

> style stick

Changed 65 atom styles  

> style sphere

Changed 65 atom styles  

> style stick

Changed 65 atom styles  

> style ball

Changed 65 atom styles  

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting full

> ui tool show "Selection Inspector"

> show surfaces

> hide surfaces

> show cartoons

> hide cartoons

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> nucleotides tube/slab shape box

> nucleotides ladder

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> color byhetero

> color bychain

> color byhetero

[Repeated 1 time(s)]

> color bypolymer

> color bychain

> color bypolymer

> rainbow

> coulombic

Coulombic values for generated by VMD_ SES surface #2.1: minimum, 0.00, mean
0.00, maximum 0.00  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

mlp: no amino acids specified  

> color bfactor

65 atoms, 4 residues, 1 surfaces, atom bfactor range 0 to 0  

> color bynucleotide

[Repeated 1 time(s)]

> color bfactor

65 atoms, 4 residues, 1 surfaces, atom bfactor range 0 to 0  

> mlp

mlp: no amino acids specified  

> coulombic

Coulombic values for generated by VMD_ SES surface #2.1: minimum, 0.00, mean
0.00, maximum 0.00  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow

> color bypolymer

> color bychain

> color byhetero

[Repeated 2 time(s)]

> style ball

Changed 65 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> color byhetero

[Repeated 1 time(s)]

> color bynucleotide

> color bfactor

65 atoms, 4 residues, 1 surfaces, atom bfactor range 0 to 0  

> mlp

mlp: no amino acids specified  

> coulombic

Coulombic values for generated by VMD_ SES surface #2.1: minimum, 0.00, mean
0.00, maximum 0.00  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow

[Repeated 1 time(s)]

> color bypolymer

[Repeated 1 time(s)]

> color bychain

[Repeated 1 time(s)]

> color byhetero

[Repeated 1 time(s)]

> undo

[Repeated 9 time(s)]

> interfaces ~solvent

0 buried areas:  

> interfaces ~solvent

0 buried areas:  

> close #2.1

> interfaces ~solvent

0 buried areas:  

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting full

> interfaces ~solvent

0 buried areas:  

> interfaces ~solvent

0 buried areas:  

> ui mousemode right distance

> distance /?:1@@serial_number=-1 /?:1@@serial_number=-1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 62 atoms and 0
measurable objects  

> ui mousemode right select

> ui mousemode right distance

[Repeated 1 time(s)]

> distance /?:1@@serial_number=-1 /?:1@@serial_number=-1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 62 atoms and 0
measurable objects  

> ui mousemode right "link markers"

[Repeated 1 time(s)]

> volume showOutlineBox true

No volumes specified  

> volume planes z style image imageMode "full region"

No volumes specified  

> volume region all imageMode "full region"

No volumes specified  

> ui tool show "Cage Builder"

> ui tool show "Crystal Contacts"

> hide target a

> show target ab

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show "Basic Actions"

> hide #2 target abp

[Repeated 3 time(s)]

> show #2 target abp

[Repeated 3 time(s)]

> hide #2 target abp

[Repeated 3 time(s)]

> show #2 target abp

[Repeated 3 time(s)]

> hide #2 target abp

[Repeated 3 time(s)]

> show #2 target abp

[Repeated 3 time(s)]

> show #2 target c

[Repeated 3 time(s)]

> hide #2 target c

[Repeated 3 time(s)]

> show #2 target s

[Repeated 3 time(s)]

> hide #2 target s

[Repeated 1 time(s)]

> ui mousemode right select

> select /?:1@@serial_number=-1

62 atoms, 74 bonds, 1 residue, 1 model selected  

> hide #2.1 models

> show #2.1 models

> close #2.1

> ui mousemode right "link markers"

> ui mousemode right "move markers"

> ui mousemode right "mark point"

> marker #1 position 9.413,4.263,3.192 color yellow radius 1

> marker #1 position 7.761,3.464,4.347 color yellow radius 1

> ui mousemode right "link markers"

> marker link #1:2,1 color #659cef radius 0.5

> ui mousemode right "move markers"

> marker change #1:2 position 7.236,3.699,4.209

> marker change #1:1 position 9.184,4.345,3.035

> marker change #1:1 position 9.095,4.241,3.118

> marker change #1:2 position 7.279,3.699,4.214

> marker change #1:2 position 7.275,3.742,4.215

> ui mousemode right "resize markers"

> marker change #1:1 radius 0.5886

> ui mousemode right "delete markers"

> marker delete #1:1

> marker delete #1:2

> ui mousemode right label

> label (#2::chain_id=' '&:1)

> label delete residues

> label (#2::chain_id=' '&:1)

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> toolshed show

Downloading bundle SEQCROW-1.7.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\samaray\downloads\seqcrow-1.7.1-py3-none-any.whl  
Requirement already satisfied: scipy in c:\program
files\chimerax\bin\lib\site-packages (from SEQCROW==1.7.1) (1.9.3)  
Requirement already satisfied: psutil in c:\program
files\chimerax\bin\lib\site-packages (from SEQCROW==1.7.1) (5.9.4)  
Collecting Send2Trash  
Downloading Send2Trash-1.8.2-py3-none-any.whl (18 kB)  
Requirement already satisfied: jinja2 in c:\program
files\chimerax\bin\lib\site-packages (from SEQCROW==1.7.1) (3.1.2)  
Requirement already satisfied: ChimeraX-Core<=1.7,>=1.3 in c:\program
files\chimerax\bin\lib\site-packages (from SEQCROW==1.7.1) (1.6.1)  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.7.1) (2.1.2)  
Requirement already satisfied: numpy<1.26.0,>=1.18.5 in c:\program
files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.7.1) (1.23.5)  
Installing collected packages: Send2Trash, SEQCROW  
Successfully installed SEQCROW-1.7.1 Send2Trash-1.8.2  
\---  

Successfully installed SEQCROW-1.7.1 Send2Trash-1.8.2  
Installed SEQCROW (1.7.1)  

> ui tool show "AaronTools Fragment Library"

> ui tool show "2D Builder"

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> ui tool show "Bond Editor"

FYI: command is replacing existing command: "~2dlabels"  

> label (#2::chain_id=' '&:1)

[Repeated 1 time(s)]

> ui mousemode right select

> select /?:1@@serial_number=-1

62 atoms, 74 bonds, 1 residue, 1 model selected  

> select /?:1@@serial_number=-1

62 atoms, 74 bonds, 1 residue, 1 model selected  

> select clear

> delete bonds sel

[Repeated 2 time(s)]

> select /?:1@@serial_number=-1

62 atoms, 74 bonds, 1 residue, 1 model selected  

> select /?:1@@serial_number=-1

62 atoms, 74 bonds, 1 residue, 1 model selected  

> undo

[Repeated 4 time(s)]

> delete bonds sel

> select clear

> select /?:1@@serial_number=-1

62 atoms, 1 residue, 1 model selected  

> select /?:1@@serial_number=-1

62 atoms, 1 residue, 1 model selected  

> select /?:1@@serial_number=-1

62 atoms, 1 residue, 1 model selected  

> select /?:1@@serial_number=-1

62 atoms, 1 residue, 1 model selected  

> open "E:/Downloads/IE/hpc/me_si/mtd_C-Si_ELT_1423K/traj_imgs/eye
> length/1155.mol2"

Opened 1155.mol2 containing 1 structures (65 atoms, 74 bonds)  

> hide #1 models

> close #2

> show #1 models

> select add #1

65 atoms, 74 bonds, 4 residues, 1 model selected  

> select subtract #1

Nothing selected  

> style ball

Changed 65 atom styles  

> lighting full

> lighting simple

> lighting soft

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> lighting full

> ui tool show "Unit Cell"

> select add #1

65 atoms, 74 bonds, 4 residues, 1 model selected  

> close

> open "E:/Downloads/IE/hpc/me_si/mtd_C-Si_ELT_1423K/traj_imgs/eye
> length/1155"

'E:/Downloads/IE/hpc/me_si/mtd_C-Si_ELT_1423K/traj_imgs/eye length/1155' has
no suffix  

> open "E:/Downloads/IE/hpc/me_si/mtd_C-Si_ELT_1423K/traj_imgs/eye
> length/1155.pdb"

> style ball

Changed 65 atom styles  

> unitcell #1 cells 2,2,2

[Repeated 1 time(s)]

> unitcell outline #1

> unitcell delete #1

[Repeated 3 time(s)]

> unitcell #1 cells 3,3,3

> ui tool show "Bond Editor"

> lighting full

> hide #1 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> view #2 clip false

> show #!2 target m

> hide #!2 target m

[Repeated 1 time(s)]

> show #!2 target m

> unitcell #1 cells 3,3,3

[Repeated 3 time(s)]

> show #2.1

> show #1 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> unitcell #1

[Repeated 1 time(s)]

> unitcell #1 cells 3,1,1 offset -1,0,0

[Repeated 2 time(s)]

> unitcell outline #1

> hide #!2 models

> show #!2 models

> hide #1 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> show #1 models

> select add #1

65 atoms, 82 bonds, 1 residue, 1 model selected  

> select add #2

130 atoms, 164 bonds, 2 residues, 3 models selected  

> select subtract #2.1

65 atoms, 82 bonds, 1 residue, 2 models selected  

> select add #2.1

130 atoms, 164 bonds, 2 residues, 3 models selected  

> select subtract #2

65 atoms, 82 bonds, 1 residue, 1 model selected  

> select subtract #1

Nothing selected  

> unitcell #1 cells 3,1,1 offset -1,0,0

[Repeated 1 time(s)]

> view

[Repeated 2 time(s)]

> view orient

> ui tool show "Side View"

> view

[Repeated 1 time(s)]

> view orient

> ui tool show "Side View"

> select #1/X:1@@serial_number=47

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=26

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=34

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=17

1 atom, 1 residue, 1 model selected  

> ui tool show "Bond Editor"

> select #1/X:1@@serial_number=34

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=17

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=34

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=17

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=17

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=34

1 atom, 1 residue, 1 model selected  

> tsbond sel color rgb(171, 255, 255) radius 0.160 transparency 75

2 atoms must be selected  

> select #1/X:1@@serial_number=17

1 atom, 1 residue, 1 model selected  

> tsbond sel color rgb(171, 255, 255) radius 0.160 transparency 75

2 atoms must be selected  

> select add #1/X:1@@serial_number=34

2 atoms, 1 residue, 1 model selected  

> tsbond sel color rgb(171, 255, 255) radius 0.160 transparency 75

> ~tsbond sel

Created 0 bonds  

> delete bonds sel

> select #1/X:1@C

1 atom, 1 residue, 1 model selected  

> select add #1/X:1@@serial_number=63

2 atoms, 1 residue, 1 model selected  

> tsbond sel color rgb(171, 255, 255) radius 0.160 transparency 75

Drag select of 2 atoms, 4 bonds  

> select clear

> lighting simple

> lighting full

> lighting simple

> lighting soft

> lighting full

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> preset "initial styles" sticks

Using preset: Initial Styles / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" sticks

Using preset: Initial Styles / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Using preset: Initial Styles / Space-Filling (Chain Colors)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (single color)"

Using preset: Initial Styles / Space-Filling (Single Color)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "initial styles" sticks

Using preset: Initial Styles / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "initial styles" sticks

Using preset: Initial Styles / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> 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

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  

> set bgColor transparent

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> set bgColor white

> set bgColor #ffffff00

> style ball

Changed 130 atom styles  

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "ball-stick-endcap 2"

Using preset: SEQCROW / Ball-Stick-Endcap 2  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "index labels"

Using preset: SEQCROW / Index Labels  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "index labels"

Using preset: SEQCROW / Index Labels  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow sticks

Using preset: SEQCROW / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "sticks 2"

Using preset: SEQCROW / Sticks 2  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select clear

> style stick

Changed 130 atom styles  

> style ball

Changed 130 atom styles  

> style stick

Changed 130 atom styles  

> style ball

Changed 130 atom styles  

> select #1/X:1@@serial_number=34

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=34

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=34

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> select #2.1/X:1@@serial_number=34

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> select #1/X:1@@serial_number=51

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> select #2.1/X:1@@serial_number=51

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> select #1/X:1@@serial_number=36

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> select #2.1/X:1@@serial_number=36

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> hide #!2 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> hide #!2 models

> show #!2 models

> show #!2.1 models

> hide #!1 models

> show #!1 models

> help help:user/preferences.html#startup

> preset seqcrow vdw

Using preset: SEQCROW / VDW  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> 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

  

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "ball-stick-endcap 2"

Using preset: SEQCROW / Ball-Stick-Endcap 2  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "ball-stick-endcap 2"

Using preset: SEQCROW / Ball-Stick-Endcap 2  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  

> set bgColor transparent

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> set bgColor white

> set bgColor #ffffff00

> lighting full

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" sticks

Using preset: Initial Styles / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "initial styles" "space-filling (single color)"

Using preset: Initial Styles / Space-Filling (Single Color)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Using preset: Initial Styles / Space-Filling (Chain Colors)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> 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

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "index labels"

Using preset: SEQCROW / Index Labels  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> hide #1.3 models

> show #1.2 models

> hide #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #!1 models

> hide #2.1.2 models

> close #2.1.2

> show #2.1.1 models

> close #2.1.1

> show #1.2 models

> hide #1.2 models

> close #1.2

> select clear

> ui tool show "Scale Bar"

> scalebar

> scalebar off

> ui tool show "Build Structure"

> unitcell #1 offset 3,3,3

> close #1.3

> hide #1.1 models

> hide #!1 models

> show #!1 models

> show #1.1 models

> hide #!1 models

> hide #1.1 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> select add #2

62 atoms, 82 bonds, 1 residue, 2 models selected  

> select subtract #2

Nothing selected  

> select add #2.1

62 atoms, 82 bonds, 1 residue, 1 model selected  

> select subtract #2.1

Nothing selected  

> select add #2.1

62 atoms, 82 bonds, 1 residue, 1 model selected  

> select subtract #2.1

Nothing selected  

> show #1.1 models

> hide #!1 models

> show #!1 models

> unitcell #1 cells 3,3,3 offset 3,3,3

[Repeated 1 time(s)]

> unitcell outline #1

[Repeated 3 time(s)]

> unitcell #1 offset 3,3,3

> unitcell #1 offset 1,1,1

> unitcell #1 cells 3,3,3 offset 1,1,1

> unitcell #1 cells 3,3,3 offset -1,-1,-1

[Repeated 1 time(s)]

> unitcell #1 cells 3,3,3 offset -3,-3,-3

> unitcell #1 cells 3,3,3

> unitcell #1 cells 3,3,3 symFromFile false spacegroup false ncs false pack
> false

> unitcell #1 cells 3,3,3 offset 1,1,1 symFromFile false spacegroup false ncs
> false pack false

> unitcell #1 cells 3,1,1 offset -1,0,0 symFromFile false spacegroup false ncs
> false pack false

> unitcell #1 cells 3,1,1 offset -1,0,0 symFromFile false spacegroup false ncs
> false

> unitcell #1 cells 3,1,1 offset -1,0,0 symFromFile false spacegroup false

> unitcell #1 cells 3,1,1 offset -1,0,0 symFromFile false

> unitcell #1 cells 3,1,1 offset -1,0,0

> unitcell outline #1

> unitcell #1 cells 3,1,1 offset -1,0,0

> ui windowfill toggle

[Repeated 1 time(s)]

> lighting shadows true

> lighting flat

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> lighting full

> lighting shadows false

> graphics silhouettes true

> select #1/X:1@@serial_number=8

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=15

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=41

1 atom, 1 residue, 1 model selected  

> select add #1/X:1@@serial_number=15

2 atoms, 1 residue, 1 model selected  

> select add #1/X:1@@serial_number=8

3 atoms, 1 residue, 1 model selected  

> select clear

> select #1/X:1@C

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/X:1@@serial_number=64

1 atom, 1 residue, 1 model selected  

> select #1/X:1@@serial_number=64

1 atom, 1 residue, 1 model selected  

> select clear

> unitcell delete #1

> unitcell #1 cells 3,1,1 offset -1,0,0

> hide #!1 models

> hide #1.1 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2 models

> show #!2 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> hide #1.1 models

> unitcell delete #1

> unitcell #1 cells 3,3,3 offset 3,3,3

> select add #2.1

62 atoms, 82 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select subtract #2.1

Nothing selected  

> select add #2

62 atoms, 82 bonds, 1 pseudobond, 1 residue, 3 models selected  

> select subtract #2

Nothing selected  

> select add #2

62 atoms, 82 bonds, 1 pseudobond, 1 residue, 3 models selected  

> select subtract #2

Nothing selected  

> hide #!2.1 models

> hide #!2 models

> show #!2 models

> show #!2.1 models

> hide #!2.1 models

> show #1.1 models

> hide #1.1 models

> hide #!1 models

> show #!2.1 models

> hide #!2 models

> hide #!2.1 models

> show #!2.1 models

> unitcell delete #1

> unitcell #1 cells 3,3,3 offset 3,3,3

> unitcell outline #1

> set bgColor black

> set bgColor transparent

> unitcell outline #1

[Repeated 1 time(s)]

> set bgColor white

> set bgColor #ffffff00

> unitcell #1 cells 3,3,3 offset 1,1,1

> unitcell delete #1

> unitcell #1 cells 3,3,3 offset 1,1,1 origin 0.5,0.5,0.5

> unitcell delete #1

> unitcell #1 cells 3,3,3 offset 1,1,1

> unitcell delete #1

> unitcell #1 cells 0,0,0

> unitcell delete #1

> unitcell #1

> unitcell outline #1

[Repeated 1 time(s)]

> unitcell #1

[Repeated 1 time(s)]




OpenGL version: 3.3.0 NVIDIA 528.49
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: bg_BG.cp1251
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Pro (Build 18362)
Memory: 34,291,228,672
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900KF CPU @ 3.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.2
    SEQCROW: 1.7.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Attachments (1)

1155.pdb​ (5.2 KB ) - added by dobromirak@… 2 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (6)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Higher-Order Structure
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → unitcell issues

Reported by Dobromir Antonov Kalchevski

comment:2 by Tom Goddard, 2 years ago

The fact that unit cell does not work with your 1155.pdb file is no doubt because of an issue with the file. If you attach the file I could look at it. There is nothing I can say about the cause of the problem without the data.

comment:3 by dobromirak@…, 2 years ago 

Hello,

I am attaching the file. The file works with VMD and the neighboring cells
are generated correctly.

Regards,
Dobromir



On Fri, Jul 7, 2023 at 9:32 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>

1155.pdb​

by dobromirak@…, 2 years ago

Attachment: 1155.pdb​ added

Added by email2trac

comment:4 by Tom Goddard, 2 years ago

If you add a line to the top of your 1155.pdb file containing REMARK then it will work.

The ChimeraX unit cell tool looked for REMARK in the headers to know if this was a PDB file, and not finding that it produced no unit cell information.

Keep in mind ChimeraX is designed to analyze protein crystals, not small molecule crystals like this. If you run "unitcell #1 cells 2,2,2" it will not add bonds between the different unit cells. To add the bonds you could combine the unit cell models into a single model with "combine #2" and then find bonds of reasonable length with "bond #3".

comment:5 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in July 9, 2023 daily build.

The unit cell tool looked for REMARK records in the atomic structure metadata to identify models coming from PDB format. This file has no REMARK records. I made unit cell also look for CRYST1 in the metadata to identify PDB format.

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