Grouping model hidden

[kristen.browne@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202210260016 (2022-10-26 00:16:05 UTC)
Description
open 2GKU
change preset to "NIH 3D>surface coulombic
Works great!
open 2GKU
change preset to NIH3D>ribbon monochrome
change preset to NIH3D>surface coulombic
Structure is gone!

Since the surfaces are generated AFTER the ribbons in NIH 3D, I think this is resulting in empty GLB files being output

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.dev202210260016 (2022-10-26)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/brownekm/Downloads/AcCAA.mol2 format mol2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\io.py", line 196, in _make_structure  
residue = substid2residue[atom_data.subst_id]  
KeyError: None  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\\__init__.py", line 59, in open  
return opener(session, data, file_name, True, True)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\io.py", line 6, in open_mol2  
p = Mol2Parser(session, stream, file_name, auto_style, atomic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\io.py", line 82, in __init__  
self._make_structure()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\viewdockx\io.py", line 199, in _make_structure  
residue = s.new_residue("UNK", '', atom_data.subst_id)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1817, in new_residue  
return f(self._c_pointer, residue_name.encode('utf-8'),
chain_id.encode('utf-8'), pos, insert.encode('utf-8'), ctypes.c_void_p(0) if
precedes is None else precedes._c_pointer)  
ctypes.ArgumentError: argument 4: <class 'TypeError'>: wrong type  
  
ctypes.ArgumentError: argument 4: : wrong type  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1817, in new_residue  
return f(self._c_pointer, residue_name.encode('utf-8'),
chain_id.encode('utf-8'), pos, insert.encode('utf-8'), ctypes.c_void_p(0) if
precedes is None else precedes._c_pointer)  
  
See log for complete Python traceback.  
  

> open 2GKU

Summary of feedback from opening 2GKU fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for DT /A:1  
note | Fetching compressed mmCIF 2gku from
http://files.rcsb.org/download/2gku.cif  
  
2gku title:  
Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two
edgewise loops and double-chain reversal loop, NMR, 12 structures [more
info...]  
  
Chain information for 2gku  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A |
Human telomere DNA  
  

> preset "initial styles" sticks

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

> 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

  

> open
> C:/Users/aabrownekm/Downloads/Basic_Webpack_x64-51.3.4843-DJP4100_Basicx64_Webpack.exe

Unrecognized file suffix '.exe'  

> open C:/Users/brownekm/Downloads/ChimeraX_NIHPresets-1.1.1-py3-none-any.whl

Unrecognized file suffix '.whl'  

> help help:user/preferences.html#startup

>

Incomplete command: toolshed  

> toolshed show

Downloading bundle ChimeraX_NIHPresets-1.1.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3  
[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\aabrownekm\downloads\chimerax_nihpresets-1.1.1-py3-none-
any.whl  
Requirement already satisfied: ChimeraX-Struts>=1.0.1,~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-NIHPresets==1.1.1) (1.0.1)  
Requirement already satisfied: ChimeraX-PresetMgr~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-NIHPresets==1.1.1) (1.1)  
Requirement already satisfied: ChimeraX-Core~=1.3 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-NIHPresets==1.1.1)
(1.6.dev202210260016)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Struts>=1.0.1,~=1.0->ChimeraX-NIHPresets==1.1.1) (1.2)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Geometry~=1.0->ChimeraX-
Struts>=1.0.1,~=1.0->ChimeraX-NIHPresets==1.1.1) (1.0)  
Installing collected packages: ChimeraX-NIHPresets  
Successfully installed ChimeraX-NIHPresets-1.1.1  
\---  

Successfully installed ChimeraX-NIHPresets-1.1.1  
Installed ChimeraX-NIHPresets (1.1.1)  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 9348 atom radii, 10104 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to 2gku #1.1  
---  
notes | Termini for 2gku (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.2  
---  
notes | Termini for 2gku (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
29 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.3  
---  
notes | Termini for 2gku (#1.3) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.4  
---  
notes | Termini for 2gku (#1.4) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.5  
---  
notes | Termini for 2gku (#1.5) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.6  
---  
notes | Termini for 2gku (#1.6) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
29 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.7  
---  
notes | Termini for 2gku (#1.7) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.8  
---  
notes | Termini for 2gku (#1.8) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.9  
---  
notes | Termini for 2gku (#1.9) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.10  
---  
notes | Termini for 2gku (#1.10) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.11  
---  
notes | Termini for 2gku (#1.11) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
28 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.12  
---  
notes | Termini for 2gku (#1.12) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 11 time(s)]Coulombic values for Surface #1.1 #1.1.1: minimum,
-23.71, mean -13.48, maximum -4.18  
Coulombic values for Surface #1.2 #1.2.1: minimum, -27.85, mean -13.74,
maximum -2.96  
Coulombic values for Surface #1.3 #1.3.1: minimum, -28.65, mean -13.83,
maximum -3.69  
Coulombic values for Surface #1.4 #1.4.1: minimum, -27.86, mean -13.68,
maximum -3.52  
Coulombic values for Surface #1.5 #1.5.1: minimum, -24.58, mean -13.66,
maximum -3.87  
Coulombic values for Surface #1.6 #1.6.1: minimum, -26.80, mean -13.82,
maximum -3.63  
Coulombic values for Surface #1.7 #1.7.1: minimum, -30.26, mean -13.76,
maximum -3.62  
Coulombic values for Surface #1.8 #1.8.1: minimum, -25.16, mean -13.67,
maximum -4.37  
Coulombic values for Surface #1.9 #1.9.1: minimum, -26.83, mean -13.67,
maximum -4.11  
Coulombic values for Surface #1.10 #1.10.1: minimum, -25.30, mean -13.64,
maximum -3.99  
Coulombic values for Surface #1.11 #1.11.1: minimum, -35.28, mean -13.72,
maximum -4.02  
Coulombic values for Surface #1.12 #1.12.1: minimum, -26.10, mean -13.72,
maximum -3.49  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    addh #1.2
    addh #1.3
    addh #1.4
    addh #1.5
    addh #1.6
    addh #1.7
    addh #1.8
    addh #1.9
    addh #1.10
    addh #1.11
    addh #1.12
    surface #1.1 enclose #1.1 grid 0.5 sharp true
    surface #1.2 enclose #1.2 grid 0.5 sharp true
    surface #1.3 enclose #1.3 grid 0.5 sharp true
    surface #1.4 enclose #1.4 grid 0.5 sharp true
    surface #1.5 enclose #1.5 grid 0.5 sharp true
    surface #1.6 enclose #1.6 grid 0.5 sharp true
    surface #1.7 enclose #1.7 grid 0.5 sharp true
    surface #1.8 enclose #1.8 grid 0.5 sharp true
    surface #1.9 enclose #1.9 grid 0.5 sharp true
    surface #1.10 enclose #1.10 grid 0.5 sharp true
    surface #1.11 enclose #1.11 grid 0.5 sharp true
    surface #1.12 enclose #1.12 grid 0.5 sharp true
    color white
    coulombic surfaces #*

  

> save 2GKU-surf-coulombic_NIH3D.glb

> save C:/Users/brownekm/Desktop/2GKU-surf-coulombic_NIH3D.glb

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 9348 atom radii, 10104 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Nothing selected  
[Repeated 1 time(s)]Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    delete H
    preset 'initial styles' cartoon
    nucleotides ladder radius 1.2
    color white target abc
    color helix marine
    color strand firebrick
    color coil goldenrod
    color nucleic-acid forest
    color :A:C:G:U grape
    color byatom
    select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide)
    color sel carbon_grey atoms
    color ligand | protein & sideonly byhet atoms
    ~select
    rainbow #1.1@ca,c4' chains palette marine:marine target rs
    rainbow #1.2@ca,c4' chains palette marine:marine target rs
    rainbow #1.3@ca,c4' chains palette marine:marine target rs
    rainbow #1.4@ca,c4' chains palette marine:marine target rs
    rainbow #1.5@ca,c4' chains palette marine:marine target rs
    rainbow #1.6@ca,c4' chains palette marine:marine target rs
    rainbow #1.7@ca,c4' chains palette marine:marine target rs
    rainbow #1.8@ca,c4' chains palette marine:marine target rs
    rainbow #1.9@ca,c4' chains palette marine:marine target rs
    rainbow #1.10@ca,c4' chains palette marine:marine target rs
    rainbow #1.11@ca,c4' chains palette marine:marine target rs
    rainbow #1.12@ca,c4' chains palette marine:marine target rs

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 6060 atom radii, 6816 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to 2gku #1.1  
---  
notes | Termini for 2gku (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.2  
---  
notes | Termini for 2gku (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
29 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.3  
---  
notes | Termini for 2gku (#1.3) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.4  
---  
notes | Termini for 2gku (#1.4) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.5  
---  
notes | Termini for 2gku (#1.5) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.6  
---  
notes | Termini for 2gku (#1.6) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
29 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.7  
---  
notes | Termini for 2gku (#1.7) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.8  
---  
notes | Termini for 2gku (#1.8) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
33 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.9  
---  
notes | Termini for 2gku (#1.9) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.10  
---  
notes | Termini for 2gku (#1.10) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.11  
---  
notes | Termini for 2gku (#1.11) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
28 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.12  
---  
notes | Termini for 2gku (#1.12) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
274 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 11 time(s)]Coulombic values for Surface #1.1 #1.1.1: minimum,
-24.37, mean -13.56, maximum -4.23  
Coulombic values for Surface #1.2 #1.2.1: minimum, -28.05, mean -13.74,
maximum -3.00  
Coulombic values for Surface #1.3 #1.3.1: minimum, -28.83, mean -13.90,
maximum -3.56  
Coulombic values for Surface #1.4 #1.4.1: minimum, -27.81, mean -13.73,
maximum -3.43  
Coulombic values for Surface #1.5 #1.5.1: minimum, -25.09, mean -13.74,
maximum -3.85  
Coulombic values for Surface #1.6 #1.6.1: minimum, -26.84, mean -13.95,
maximum -3.76  
Coulombic values for Surface #1.7 #1.7.1: minimum, -28.01, mean -13.85,
maximum -3.69  
Coulombic values for Surface #1.8 #1.8.1: minimum, -27.82, mean -13.71,
maximum -4.12  
Coulombic values for Surface #1.9 #1.9.1: minimum, -27.20, mean -13.66,
maximum -4.05  
Coulombic values for Surface #1.10 #1.10.1: minimum, -25.72, mean -13.65,
maximum -4.08  
Coulombic values for Surface #1.11 #1.11.1: minimum, -32.39, mean -13.72,
maximum -4.03  
Coulombic values for Surface #1.12 #1.12.1: minimum, -26.95, mean -13.76,
maximum -3.62  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    addh #1.2
    addh #1.3
    addh #1.4
    addh #1.5
    addh #1.6
    addh #1.7
    addh #1.8
    addh #1.9
    addh #1.10
    addh #1.11
    addh #1.12
    surface #1.1 enclose #1.1 grid 0.5 sharp true
    surface #1.2 enclose #1.2 grid 0.5 sharp true
    surface #1.3 enclose #1.3 grid 0.5 sharp true
    surface #1.4 enclose #1.4 grid 0.5 sharp true
    surface #1.5 enclose #1.5 grid 0.5 sharp true
    surface #1.6 enclose #1.6 grid 0.5 sharp true
    surface #1.7 enclose #1.7 grid 0.5 sharp true
    surface #1.8 enclose #1.8 grid 0.5 sharp true
    surface #1.9 enclose #1.9 grid 0.5 sharp true
    surface #1.10 enclose #1.10 grid 0.5 sharp true
    surface #1.11 enclose #1.11 grid 0.5 sharp true
    surface #1.12 enclose #1.12 grid 0.5 sharp true
    color white
    coulombic surfaces #*

  

> open 2GKU

Summary of feedback from opening 2GKU fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for DT /A:1  
  
2gku title:  
Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two
edgewise loops and double-chain reversal loop, NMR, 12 structures [more
info...]  
  
Chain information for 2gku  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A |
Human telomere DNA  
  

> close session

> open 2GKU

Summary of feedback from opening 2GKU fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for DT /A:1  
  
2gku title:  
Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two
edgewise loops and double-chain reversal loop, NMR, 12 structures [more
info...]  
  
Chain information for 2gku  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A |
Human telomere DNA  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 9348 atom radii, 10104 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to 2gku #1.1  
---  
notes | Termini for 2gku (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.2  
---  
notes | Termini for 2gku (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
29 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.3  
---  
notes | Termini for 2gku (#1.3) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.4  
---  
notes | Termini for 2gku (#1.4) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.5  
---  
notes | Termini for 2gku (#1.5) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.6  
---  
notes | Termini for 2gku (#1.6) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
29 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.7  
---  
notes | Termini for 2gku (#1.7) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.8  
---  
notes | Termini for 2gku (#1.8) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.9  
---  
notes | Termini for 2gku (#1.9) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.10  
---  
notes | Termini for 2gku (#1.10) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.11  
---  
notes | Termini for 2gku (#1.11) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
28 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.12  
---  
notes | Termini for 2gku (#1.12) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 11 time(s)]Coulombic values for Surface #1.1 #1.1.1: minimum,
-23.71, mean -13.48, maximum -4.18  
Coulombic values for Surface #1.2 #1.2.1: minimum, -27.85, mean -13.74,
maximum -2.96  
Coulombic values for Surface #1.3 #1.3.1: minimum, -28.65, mean -13.83,
maximum -3.69  
Coulombic values for Surface #1.4 #1.4.1: minimum, -27.86, mean -13.68,
maximum -3.52  
Coulombic values for Surface #1.5 #1.5.1: minimum, -24.58, mean -13.66,
maximum -3.87  
Coulombic values for Surface #1.6 #1.6.1: minimum, -26.80, mean -13.82,
maximum -3.63  
Coulombic values for Surface #1.7 #1.7.1: minimum, -30.26, mean -13.76,
maximum -3.62  
Coulombic values for Surface #1.8 #1.8.1: minimum, -25.16, mean -13.67,
maximum -4.37  
Coulombic values for Surface #1.9 #1.9.1: minimum, -26.83, mean -13.67,
maximum -4.11  
Coulombic values for Surface #1.10 #1.10.1: minimum, -25.30, mean -13.64,
maximum -3.99  
Coulombic values for Surface #1.11 #1.11.1: minimum, -35.28, mean -13.72,
maximum -4.02  
Coulombic values for Surface #1.12 #1.12.1: minimum, -26.10, mean -13.72,
maximum -3.49  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    addh #1.2
    addh #1.3
    addh #1.4
    addh #1.5
    addh #1.6
    addh #1.7
    addh #1.8
    addh #1.9
    addh #1.10
    addh #1.11
    addh #1.12
    surface #1.1 enclose #1.1 grid 0.5 sharp true
    surface #1.2 enclose #1.2 grid 0.5 sharp true
    surface #1.3 enclose #1.3 grid 0.5 sharp true
    surface #1.4 enclose #1.4 grid 0.5 sharp true
    surface #1.5 enclose #1.5 grid 0.5 sharp true
    surface #1.6 enclose #1.6 grid 0.5 sharp true
    surface #1.7 enclose #1.7 grid 0.5 sharp true
    surface #1.8 enclose #1.8 grid 0.5 sharp true
    surface #1.9 enclose #1.9 grid 0.5 sharp true
    surface #1.10 enclose #1.10 grid 0.5 sharp true
    surface #1.11 enclose #1.11 grid 0.5 sharp true
    surface #1.12 enclose #1.12 grid 0.5 sharp true
    color white
    coulombic surfaces #*

  

> close session

> open 2GKU

Summary of feedback from opening 2GKU fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for DT /A:1  
  
2gku title:  
Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two
edgewise loops and double-chain reversal loop, NMR, 12 structures [more
info...]  
  
Chain information for 2gku  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A |
Human telomere DNA  
  

> preset nih3d "ribbon monochrome"

Using preset: NIH3D / Ribbon Monochrome  
Changed 9348 atom radii, 10104 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Nothing selected  
[Repeated 1 time(s)]Assigning color attribute to 0 items  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    delete H
    preset 'initial styles' cartoon
    nucleotides ladder radius 1.2
    color white target abc
    color helix marine
    color strand firebrick
    color coil goldenrod
    color nucleic-acid forest
    color :A:C:G:U grape
    color byatom
    select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide)
    color sel carbon_grey atoms
    color ligand | protein & sideonly byhet atoms
    ~select
    color nih_blue
    setattr p color nih_blue

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 6060 atom radii, 6816 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to 2gku #1.1  
---  
notes | Termini for 2gku (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.2  
---  
notes | Termini for 2gku (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
29 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.3  
---  
notes | Termini for 2gku (#1.3) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.4  
---  
notes | Termini for 2gku (#1.4) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.5  
---  
notes | Termini for 2gku (#1.5) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.6  
---  
notes | Termini for 2gku (#1.6) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
29 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.7  
---  
notes | Termini for 2gku (#1.7) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.8  
---  
notes | Termini for 2gku (#1.8) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
33 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.9  
---  
notes | Termini for 2gku (#1.9) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.10  
---  
notes | Termini for 2gku (#1.10) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.11  
---  
notes | Termini for 2gku (#1.11) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
28 hydrogen bonds  
274 hydrogens added  
  
Summary of feedback from adding hydrogens to 2gku #1.12  
---  
notes | Termini for 2gku (#1.12) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
274 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 11 time(s)]Coulombic values for Surface #1.1 #1.1.1: minimum,
-24.37, mean -13.56, maximum -4.23  
Coulombic values for Surface #1.2 #1.2.1: minimum, -28.05, mean -13.74,
maximum -3.00  
Coulombic values for Surface #1.3 #1.3.1: minimum, -28.83, mean -13.90,
maximum -3.56  
Coulombic values for Surface #1.4 #1.4.1: minimum, -27.81, mean -13.73,
maximum -3.43  
Coulombic values for Surface #1.5 #1.5.1: minimum, -25.09, mean -13.74,
maximum -3.85  
Coulombic values for Surface #1.6 #1.6.1: minimum, -26.84, mean -13.95,
maximum -3.76  
Coulombic values for Surface #1.7 #1.7.1: minimum, -28.01, mean -13.85,
maximum -3.69  
Coulombic values for Surface #1.8 #1.8.1: minimum, -27.82, mean -13.71,
maximum -4.12  
Coulombic values for Surface #1.9 #1.9.1: minimum, -27.20, mean -13.66,
maximum -4.05  
Coulombic values for Surface #1.10 #1.10.1: minimum, -25.72, mean -13.65,
maximum -4.08  
Coulombic values for Surface #1.11 #1.11.1: minimum, -32.39, mean -13.72,
maximum -4.03  
Coulombic values for Surface #1.12 #1.12.1: minimum, -26.95, mean -13.76,
maximum -3.62  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    addh #1.2
    addh #1.3
    addh #1.4
    addh #1.5
    addh #1.6
    addh #1.7
    addh #1.8
    addh #1.9
    addh #1.10
    addh #1.11
    addh #1.12
    surface #1.1 enclose #1.1 grid 0.5 sharp true
    surface #1.2 enclose #1.2 grid 0.5 sharp true
    surface #1.3 enclose #1.3 grid 0.5 sharp true
    surface #1.4 enclose #1.4 grid 0.5 sharp true
    surface #1.5 enclose #1.5 grid 0.5 sharp true
    surface #1.6 enclose #1.6 grid 0.5 sharp true
    surface #1.7 enclose #1.7 grid 0.5 sharp true
    surface #1.8 enclose #1.8 grid 0.5 sharp true
    surface #1.9 enclose #1.9 grid 0.5 sharp true
    surface #1.10 enclose #1.10 grid 0.5 sharp true
    surface #1.11 enclose #1.11 grid 0.5 sharp true
    surface #1.12 enclose #1.12 grid 0.5 sharp true
    color white
    coulombic surfaces #*

  




OpenGL version: 3.3.0 NVIDIA 466.47
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 137,220,087,808
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.43.2
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202210260016
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.25
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.5
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.10.0

[Eric Pettersen]

2GKU is an NMR ensemble (which the NIH3D script deletes all but one model of) which means it is a hierarchy consisting of a "grouping model" whose only function is to contain the child structure models. This command in the coulombic preset causes the grouping model to be hidden:

hide H|ligand|~(protein|nucleic-acid)

So the first thing we need to do is figure out if that command should or should not hide the grouping model. Then, depending on that, either fix ChimeraX or fix the preset.

[Eric Pettersen]

The minimal formula to replicate is:

open 2gku
hide ~nucleic-acid

[Tom Goddard]

The hide command is only supposed to hide atoms if some atoms are specified. For the case you describe it seems there are atoms (there are H atoms in this structure) so the following commands work as expected and the model is not hidden.

open 2gku
close #1.2-12
hide H|ligand|~(protein|nucleic-acid)

So I am not sure what is going on -- maybe the preset does other things that are important. If no atoms are specified with the hide command then it defaults to hiding models. So if there is no H and no ligand and ~(protein|nucleic) ends up selecting the grouping model and other non-atomic models, then those models would be hidden. So I think the problem is with the preset use of this hide command. It could be argued that the hide command default is not good but I think it is ok.

[Tom Goddard]

True if the invert operator produces no atoms as the following does since all atoms are nucleic

hide ~nucleic

then the default hide behavior with no atoms specified is to hide models, and the grouping model is one of those specified by ~nucleic as are all models that are not atomic models. If the negation operator "~" operates on all open models this is what you get. The following command does the right thing

hide #1.1 & ~nucleic

[Eric Pettersen]

This seems like something that needs fixing. It's kind of ridiculous that "hide ~nucleic" hides a nucleic structure that's grouped (but not one that's not!). Completely unexpected behavior.

[Eric Pettersen]

The problem is that the selector being using (~nucleic) is atom-based (rather than model-based), but the hide function only has access to the results of the selection (atoms, residues, models) rather than the original selector. Since the selector selects no atoms, the function has to guess what level to apply the hide to, and it guesses model-level, which is usually right when no atoms get selected but is not right in this case.

Since a preset cannot possibly intersect the spec with a particular model number, I think the right approach is to explicitly tell the hide command what level to hide, i.e. the works:

open 2gku
hide ~nucleic-acid atoms

I will be modifying the presets bundle to do this and will update this ticket when that happens.

[Eric Pettersen]

The fixed bundle is on the Toolshed now. Will mail the wheel separately.