Opened 3 years ago

Closed 3 years ago

#8200 closed defect (not a bug)

Hydrogen bonded to atom that should not have hydrogens

Reported by: kristen.browne@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc: michal.stolarczyk@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202212150508 (2022-12-15 05:08:50 UTC)
Description
As shown in logs.  In NIH 3D this is causing a failure when, if the coulombic is failing for whatever reason, it should just skip it and move on.  The two errors that come up in NIH 3D are: NIH3D WARNING: Cannot execute ChimeraX preset 'surface coulombic' due to error: Hydrogen /A G 1 HP3 bonded to atom that should not have hydrogens (/A G 1 OP3); NIH3D INFO: Saving error in /tmp/nih3d_job_ww7kqlk1/messages.json: Cannot execute ChimeraX preset 'surface coulombic' due to error: Hydrogen /A G 1 HP3 bonded to atom that should not have hydrogens (/A G 1 OP3)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.dev202212150508 (2022-12-15)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX-Daily\bin\ChimeraX.exe -m
pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting ChimeraX-NIHPresets==1.1.8  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxnihpresets/releases/1.1.8/ChimeraX_NIHPresets-1.1.8-py3-none-
any.whl (7.0 kB)  
Installing collected packages: ChimeraX-NIHPresets  
Attempting uninstall: ChimeraX-NIHPresets  
Found existing installation: ChimeraX-NIHPresets 1.1.7  
Uninstalling ChimeraX-NIHPresets-1.1.7:  
Successfully uninstalled ChimeraX-NIHPresets-1.1.7  
Successfully installed ChimeraX-NIHPresets-1.1.8  
\---  

Successfully installed ChimeraX-NIHPresets-1.1.8  
Installed ChimeraX-NIHPresets (1.1.8)  

> open 2JTN

Summary of feedback from opening 2JTN fetched from pdb  
---  
note | Fetching compressed mmCIF 2jtn from
http://files.rcsb.org/download/2jtn.cif  
  
2jtn title:  
NMR Solution Structure of a ldb1-LID:Lhx3-LIM complex [more info...]  
  
Chain information for 2jtn  
---  
Chain | Description | UniProt  
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
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | LIM domain-binding
protein 1, LIM/homeobox protein Lhx3 | LHX3_MOUSE  
  

> close #1.2-20

> preset nih3d "ribbon by chain (printable)"

Using preset: NIH3D / Ribbon by Chain (Printable)  
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.  
873 atoms, 683 bonds, 182 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 4 atom radii  
728 atoms, 727 bonds, 182 residues, 1 model selected  
35 hydrogen bonds found  
Changed 51 pseudobond radii  
Created 3 struts for @ca | ligand | P, max length 8, max loop length 60  
  
Nothing selected  
Changed 1438 bond radii  
Changed 3 pseudobond dashes  
Preset expands to these ChimeraX commands:

    
    
    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
    size min-backbone pseudobondRadius 1.1
    size ions atomRadius +0.8
    select backbone & protein | nucleic-acid & min-backbone | ions | ligand | ligand :< 5 & ~nucleic-acid
    hbonds sel color white restrict both
    size pseudobondRadius 0.6
    wait 1
    struts @ca|ligand|P length 8 loop 60 rad 0.75 color struts_grey
    ~struts @PB,PG resetRibbon false
    ~struts adenine|cytosine|guanine|thymine|uracil resetRibbon false
    color hbonds white pseudobonds
    ~select
    size stickRadius 0.8
    style dashes 0

  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 1413 atom radii, 1438 bond radii, 16 pseudobond radii  
Changed 1 pseudobond dash  
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.  
873 atoms, 683 bonds, 182 residues, 1 model selected  
Nothing selected  
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

  

> preset "initial styles" "original look"

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

> preset nih3d "sticks monochrome"

Using preset: NIH3D / Sticks Monochrome  
Changed 1413 atom radii, 1438 bond radii, 16 pseudobond radii  
Changed 1 pseudobond dash  
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.  
Changed 1413 atom styles  
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'
    style stick
    ~nuc
    ~ribbon
    disp
    color nih_blue

  

> preset nih3d "surface by chain"

Using preset: NIH3D / Surface by Chain  
Changed 1413 atom radii, 1438 bond radii, 16 pseudobond radii  
Changed 1 pseudobond dash  
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 2jtn #1.1  
---  
notes | Termini for 2jtn (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 182  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLN 182  
62 hydrogen bonds  
1346 hydrogens added  
  
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) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    surface #1.1 enclose #1.1 grid 0.650142 sharp true
    rainbow #1.1@ca,c4' chains palette marine:marine target rsa
    color zone #1.1 near #1.1 & main distance 20

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 2760 atom radii, 2785 bond radii, 16 pseudobond radii  
Changed 1 pseudobond dash  
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 2jtn #1.1  
---  
notes | Termini for 2jtn (#1.1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 182  
Chain-final residues that are not actual C termini:  
58 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Surface #1.1 #1.1.2: minimum, -16.72, mean -1.23, maximum
28.34  
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) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    surface #1.1 enclose #1.1 grid 0.940909 sharp true
    color white
    coulombic surfaces #* chargeMethod gasteiger

  

> close session

> open "C:/Users/brownekm/Downloads/emd_7037_0 (1).map"

Opened emd_7037_0 (1).map as #1, grid size 320,320,320, pixel 1.06, shown at
level 0.121, step 2, values float32  

> volume #1 level 0.137

> volume #1 level 0.162

> preset nih3d "volume radial"

Using preset: NIH3D / Volume Radial  
Enclosed volume for surface (#1.1) = 1.61e+05  
Enclosed volume for surface (#1.1) = 1.375e+05  
Changed 0 atom radii, 0 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.  
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'
    volume #1 region all style surface step 1 limitVoxelCount false
    wait 1
    surface dust #1.1 size 1 metric 'size rank'
    color radial #1 palette red:yellow:green:cyan:blue center #1

  

> preset nih3d "volume monochrome"

Using preset: NIH3D / Volume Monochrome  
Enclosed volume for surface (#1.1) = 1.61e+05  
Enclosed volume for surface (#1.1) = 1.375e+05  
Changed 0 atom radii, 0 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.  
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'
    volume #1 region all style surface step 1 limitVoxelCount false
    wait 1
    surface dust #1.1 size 1 metric 'size rank'
    color nih_blue

  

> preset nih3d "volume radial"

Using preset: NIH3D / Volume Radial  
Enclosed volume for surface (#1.1) = 1.61e+05  
Enclosed volume for surface (#1.1) = 1.375e+05  
Changed 0 atom radii, 0 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.  
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'
    volume #1 region all style surface step 1 limitVoxelCount false
    wait 1
    surface dust #1.1 size 1 metric 'size rank'
    color radial #1 palette red:yellow:green:cyan:blue center #1

  

> preset "initial styles" "original look"

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

> close session

> open "C:\Users\brownekm\Downloads\emd_7037_0 (1).map" format ccp4

Opened emd_7037_0 (1).map as #1, grid size 320,320,320, pixel 1.06, shown at
level 0.121, step 2, values float32  

> volume #1 level 0.162

> preset "initial styles" "original look"

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

> volume #1 region all style surface level 1 limitVoxelCount true voxelLimit 8

> close session

> open "C:\Users\brownekm\Downloads\emd_7037_0 (1).map" format ccp4

Opened emd_7037_0 (1).map as #1, grid size 320,320,320, pixel 1.06, shown at
level 0.121, step 2, values float32  

> ~struts

> ~hbonds

> size atomRadius default stickRadius 0.2 pseudobondRadius 0.2

Changed 0 atom radii, 0 bond radii, 0 pseudobond radii  

> style dashes 7

Changed 0 pseudobond dashes  

> graphics bgColor white

> color name marine 0,50,100

Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  

> color name forest 13.3,54.5,13.3

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

  

> color name tangerine 95.3,51.8,0

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

  

> color name grape 64.3,0,86.7

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

  

> color name nih_blue 12.5,33.3,54.1

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

  

> color name jmol_carbon 56.5,56.5,56.5

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

  

> color name bond_purple 57.6,43.9,85.9

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

  

> color name struts_grey 48,48,48

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

  

> color name carbon_grey 22.2,22.2,22.2

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

  

> surface close

> preset "initial styles" 'original look'

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

> volume #1 region all style surface level 1 limitVoxelCount true voxelLimit 8

> wait 1

> surface dust #1.1 size 1 metric "size rank"

> close session

> open "C:\Users\brownekm\Downloads\emd_7037_0 (1).map" format ccp4

Opened emd_7037_0 (1).map as #1, grid size 320,320,320, pixel 1.06, shown at
level 0.121, step 2, values float32  

> volume #1.1 region all style surface level 1 limitVoxelCount true voxelLimit
> 8

No volumes specified  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  

> close session

> open "C:/Users/brownekm/Downloads/4323526 (1).cif"

Summary of feedback from opening C:/Users/brownekm/Downloads/4323526 (1).cif  
---  
note | Not a mmCIF file. Trying as a small molecule CIF file. Next time use:
open 4323526 (1).cif format corecif.  
  
  
  
4323526 (1).cif title:  
10-chloro cyanocobalamin solvate [more info...]  
  

> close session

> open C:/Users/brownekm/Downloads/HAG1.pdb

Chain information for HAG1.pdb #1  
---  
Chain | Description  
? | No description available  
  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 4433 atom radii, 4517 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.  
2747 atoms, 2159 bonds, 568 residues, 1 model selected  
Nothing selected  
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@ca,c4' chains palette marine:marine target rs

  

> preset nih3d "ribbon by chain (printable)"

Using preset: NIH3D / Ribbon by Chain (Printable)  
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.  
2747 atoms, 2159 bonds, 568 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 0 atom radii  
2272 atoms, 2271 bonds, 568 residues, 1 model selected  
221 hydrogen bonds found  
Changed 221 pseudobond radii  
Created 35 struts for @ca | ligand | P, max length 8, max loop length 60  
  
Nothing selected  
Changed 4517 bond radii  
Changed 2 pseudobond dashes  
Preset expands to these ChimeraX commands:

    
    
    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@ca,c4' chains palette marine:marine target rs
    size min-backbone pseudobondRadius 1.1
    size ions atomRadius +0.8
    select backbone & protein | nucleic-acid & min-backbone | ions | ligand | ligand :< 5 & ~nucleic-acid
    hbonds sel color white restrict both
    size pseudobondRadius 0.6
    wait 1
    struts @ca|ligand|P length 8 loop 60 rad 0.75 color struts_grey
    ~struts @PB,PG resetRibbon false
    ~struts adenine|cytosine|guanine|thymine|uracil resetRibbon false
    color hbonds white pseudobonds
    ~select
    size stickRadius 0.8
    style dashes 0

  

> preset nih3d "surface by chain"

Using preset: NIH3D / Surface by Chain  
Changed 4433 atom radii, 4517 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 HAG1.pdb #1  
---  
notes | No usable SEQRES records for HAG1.pdb (#1) chain (blank); guessing
termini instead  
Chain-initial residues that are actual N termini: /? MET 1  
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: /? GLN 568  
339 hydrogen bonds  
/? GLN 568 is not terminus, removing H atom from 'C'  
4322 hydrogens added  
  
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) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 1.1467 sharp true
    rainbow #1@ca,c4' chains palette marine:marine target rsa
    color zone #1 near #1 & main distance 20

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 8755 atom radii, 8839 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 HAG1.pdb #1  
---  
notes | No usable SEQRES records for HAG1.pdb (#1) chain (blank); guessing
termini instead  
Chain-initial residues that are actual N termini: /? MET 1  
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: /? GLN 568  
298 hydrogen bonds  
/? GLN 568 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Surface #1 #1.1: minimum, -23.33, mean -0.78, maximum
17.31  
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) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 1.44226 sharp true
    color white
    coulombic surfaces #* chargeMethod gasteiger

  

> preset nih3d "surface hydrophobicity"

Using preset: NIH3D / Surface Hydrophobicity  
Changed 8755 atom radii, 8839 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 HAG1.pdb #1  
---  
notes | No usable SEQRES records for HAG1.pdb (#1) chain (blank); guessing
termini instead  
Chain-initial residues that are actual N termini: /? MET 1  
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: /? GLN 568  
298 hydrogen bonds  
/? GLN 568 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  
568 residues, 1 surfaces, atom kd_hydrophobicity range -4.5 to 4.5  
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) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 1.44226 sharp true
    color magenta
    color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta

  

> open 4ykj

Summary of feedback from opening 4ykj fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for ALA /A:301  
Atom H1 is not in the residue template for GLY /A:302  
Atom H1 is not in the residue template for ALA /B:301  
Atom H1 is not in the residue template for GLY /B:302  
note | Fetching compressed mmCIF 4ykj from
http://files.rcsb.org/download/4ykj.cif  
  
4ykj title:  
Mnemiopsis leidyi ML032222a iGluR LBD complex with Alanine [more info...]  
  
Chain information for 4ykj #2  
---  
Chain | Description  
A B | ML032222a iGluR  
  
Non-standard residues in 4ykj #2  
---  
ALA — alanine  
GLY — glycine  
  

> close session

> open 4ykj format mmcif fromDatabase pdb

Summary of feedback from opening 4ykj fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for ALA /A:301  
Atom H1 is not in the residue template for GLY /A:302  
Atom H1 is not in the residue template for ALA /B:301  
Atom H1 is not in the residue template for GLY /B:302  
  
4ykj title:  
Mnemiopsis leidyi ML032222a iGluR LBD complex with Alanine [more info...]  
  
Chain information for 4ykj #1  
---  
Chain | Description  
A B | ML032222a iGluR  
  
Non-standard residues in 4ykj #1  
---  
ALA — alanine  
GLY — glycine  
  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 8741 atom radii, 8004 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.  
2556 atoms, 2058 bonds, 506 residues, 1 model selected  
Nothing selected  
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@ca,c4' chains palette marine:goldenrod target rs

  

> preset nih3d "ribbon by polymer (printable)"

Using preset: NIH3D / Ribbon by Polymer (Printable)  
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.  
2556 atoms, 2058 bonds, 506 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 0 atom radii  
2008 atoms, 2006 bonds, 502 residues, 1 model selected  
269 hydrogen bonds found  
Changed 269 pseudobond radii  
Created 21 struts for @ca | ligand | P, max length 8, max loop length 60  
  
Nothing selected  
Changed 4115 bond radii  
Changed 2 pseudobond dashes  
Preset expands to these ChimeraX commands:

    
    
    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
    size min-backbone pseudobondRadius 1.1
    size ions atomRadius +0.8
    select backbone & protein | nucleic-acid & min-backbone | ions | ligand | ligand :< 5 & ~nucleic-acid
    hbonds sel color white restrict both
    size pseudobondRadius 0.6
    wait 1
    struts @ca|ligand|P length 8 loop 60 rad 0.75 color struts_grey
    ~struts @PB,PG resetRibbon false
    ~struts adenine|cytosine|guanine|thymine|uracil resetRibbon false
    color hbonds white pseudobonds
    ~select
    color bypolymer
    size stickRadius 0.8
    style dashes 0

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 4028 atom radii, 4115 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 4ykj #1  
---  
notes | Termini for 4ykj (#1) chain A determined from SEQRES records  
Termini for 4ykj (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /B GLY 1, /A ALA 301, /A GLY
302, /B ALA 301, /B GLY 302  
Chain-initial residues that are not actual N termini: /A LEU 5  
Chain-final residues that are actual C termini: /A ALA 301, /A GLY 302, /B ALA
301, /B GLY 302  
Chain-final residues that are not actual C termini: /A GLY 251, /B CYS 255  
512 hydrogen bonds  
Adding 'H' to /A LEU 5  
/A GLY 251 is not terminus, removing H atom from 'C'  
/B CYS 255 is not terminus, removing H atom from 'C'  
3892 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for Surface #1 #1.1: minimum, -19.07, mean -4.43, maximum
12.73  
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) atoms
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 1.10509 sharp true
    color white
    coulombic surfaces #* chargeMethod gasteiger

  

> open pdbe_bio:3Q6X

No biogical assemblies available for 3Q6X  

> close session

> open 1TRA

Summary of feedback from opening 1TRA fetched from pdb  
---  
notes | Fetching compressed mmCIF 1tra from
http://files.rcsb.org/download/1tra.cif  
Fetching CCD 2MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/2MG/2MG.cif  
Fetching CCD H2U from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/H2U/H2U.cif  
Fetching CCD M2G from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/M2G/M2G.cif  
Fetching CCD OMC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/OMC/OMC.cif  
Fetching CCD OMG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif  
Fetching CCD YG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/YG/YG.cif  
Fetching CCD 5MC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/5MC/5MC.cif  
Fetching CCD 7MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/7MG/7MG.cif  
Fetching CCD 5MU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/5MU/5MU.cif  
Fetching CCD 1MA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/1MA/1MA.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
1tra title:  
Restrained refinement of the monoclinic form of yeast phenylalanine transfer
RNA. Temperature factors and dynamics, coordinated waters, and base-pair
propeller twist angles [more info...]  
  
Chain information for 1tra #1  
---  
Chain | Description  
A | TRNAPHE  
  
Non-standard residues in 1tra #1  
---  
MG — magnesium ion  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 1767 atom radii, 1845 bond radii, 20 pseudobond radii  
Changed 1 pseudobond dash  
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 1tra #1  
---  
notes | Termini for 1tra (#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:  
148 hydrogen bonds  
862 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen /A G 1 HP3 bonded to atom that should not have hydrogens (/A G 1 OP3)  




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 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.1
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: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5.7
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.3.1
    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: 1.43.4
    ChimeraX-AtomicLibrary: 9.0
    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: 2.7.2
    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: 1.3.1
    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.dev202212150508
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 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: 1.1.3
    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: 1.0.1
    ChimeraX-MatchMaker: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.10
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
    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: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1.8
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.3
    ChimeraX-PDB: 2.6.9
    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: 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
    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: 1.10.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.4
    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: 1.25.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.6
    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
    comm: 0.1.2
    comtypes: 1.1.10
    contourpy: 1.0.6
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.19.2
    ipython: 8.7.0
    ipython-genutils: 0.2.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 7.4.8
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.6.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.8
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 22.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.6.0
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    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: 6.4.0
    PyQt6-Qt6: 6.4.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.1
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.3
    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: 0.6.2
    tables: 3.7.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.7.1
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Change History (4)

comment:1 by pett, 3 years ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Hydrogen bonded to atom that should not have hydrogens

comment:2 by pett, 3 years ago

Cc: michal.stolarczyk@… added
Status: accepted → feedback

The script is supposed to continue on after logging such failure messages. Michal added logging those to the JSON output as errors despite them being logged to standard output as warnings. If it the fact that they are being logged as errors that leads you to believe the script stopped, or is there other evidence?

in reply to:  3 ; comment:3 by kristen.browne@…, 3 years ago 

Oh you're right!  It looks like a problem on our end. I'll check with Michal

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Thursday, December 15, 2022 5:51 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; Stolarczyk, Michal (NIH/NIAID) [C] <michal.stolarczyk@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8200: Hydrogen bonded to atom that should not have hydrogens

#8200: Hydrogen bonded to atom that should not have hydrogens
----------------------------------------+----------------------
          Reporter:  kristen.browne@...   |      Owner:  pett
              Type:  defect             |     Status:  feedback
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------
Changes (by pett):

 * cc: michal.stolarczyk@... (added)
 * status:  accepted => feedback


Comment:

 The script is supposed to continue on after logging such failure messages.
 Michal added logging those to the JSON output as errors despite them being  logged to standard output as warnings.  If it the fact that they are being  logged as errors that leads you to believe the script stopped, or is there  other evidence?

--
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comment:4 by pett, 3 years ago

Resolution: → not a bug
Status: feedback → closed
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