Bad formal charge estimate

[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
loaded attached file and switched to the coulombic preset.  Looks like a different error than we've been seeing for other problems with the coulombic preset.
The outputs from ChimeraX in 3DPX:https://3dprint.nih.gov/discover/3DPX-008738

Log:
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 2APH

2aph title:  
Crystal structure of human PGRP-IalphaC in complex with muramyl pentapeptide
[more info...]  
  
Chain information for 2aph #1  
---  
Chain | Description | UniProt  
A B | Peptidoglycan recognition protein I-alpha | PGRP3_HUMAN  
C D | muramyl pentapeptide |  
  
Non-standard residues in 2aph #1  
---  
AMU — N-acetyl-beta-muramic acid  
NH2 — amino group  
SO4 — sulfate ion  
  
2aph mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 2919 atom radii, 2766 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 2aph #1  
---  
notes | Termini for 2aph (#1) chain A determined from SEQRES records  
Termini for 2aph (#1) chain B determined from SEQRES records  
Termini for 2aph (#1) chain C determined from SEQRES records  
Termini for 2aph (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 177, /B VAL 177, /C
AMU 883, /D AMU 994  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 341, /B HIS 341, /C NH2
889, /D NH2 1000  
Chain-final residues that are not actual C termini:  
313 hydrogen bonds  
2590 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue DAL+DAL (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpjh8sxoxw\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpjh8sxoxw\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n  
(DAL+DAL) ``  
(DAL+DAL) `Welcome to antechamber 20.0: molecular input file processor.`  
(DAL+DAL) ``  
(DAL+DAL) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpjh8sxoxw\ante.in.mol2); atoms read
(29), bonds read (28).`  
(DAL+DAL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) ``  
(DAL+DAL) ``  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) `Info: Total number of electrons: 108; net charge: 0`  
(DAL+DAL) ``  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) ``  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) ``  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) ``  
Charges for residue DAL+DAL determined  
Assigning partial charges to residue AMU+ALA (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmp8avwe0ih\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmp8avwe0ih\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n  
(AMU+ALA) ``  
(AMU+ALA) `Welcome to antechamber 20.0: molecular input file processor.`  
(AMU+ALA) ``  
(AMU+ALA) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmp8avwe0ih\ante.in.mol2); atoms read
(53), bonds read (53).`  
(AMU+ALA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) ``  
(AMU+ALA) ``  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) `Info: Total number of electrons: 202; net charge: 0`  
(AMU+ALA) ``  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) ``  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) ``  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) ``  
Charges for residue AMU+ALA determined  
Assigning partial charges to residue GMA+LYS (net charge +1) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmps7mnunn7\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmps7mnunn7\ante.out.mol2 -fo mol2 -c
bcc -nc 1 -j 5 -s 2 -dr n  
(GMA+LYS) ``  
(GMA+LYS) `Welcome to antechamber 20.0: molecular input file processor.`  
(GMA+LYS) ``  
(GMA+LYS) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmps7mnunn7\ante.in.mol2); atoms read
(51), bonds read (50).`  
(GMA+LYS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) ``  
(GMA+LYS) ``  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) `Info: Total number of electrons: 178; net charge: 1`  
(GMA+LYS) ``  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) ``  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) ``  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) ``  
Charges for residue GMA+LYS determined  
Coulombic values for Surface #1 #1.1: minimum, -14.55, mean -0.20, maximum
23.17  
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
    surface #1 enclose #1 grid 0.965234 sharp true
    color white
    coulombic surfaces #*

  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 5278 atom radii, 5356 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.  
1710 atoms, 1368 bonds, 342 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:firebrick:forest 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.  
1710 atoms, 1368 bonds, 342 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 0 atom radii  
1364 atoms, 1358 bonds, 342 residues, 1 model selected  
189 hydrogen bonds found  
Changed 189 pseudobond radii  
Created 11 struts for @ca | ligand | P | ##num_atoms<500, max length 8, max
loop length 60  
  
Nothing selected  
Changed 2766 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:goldenrod:firebrick:forest 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|##num_atoms<500 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 secondary structure"

Using preset: NIH3D / Ribbon by Secondary Structure  
Changed 2688 atom radii, 2766 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.  
1710 atoms, 1368 bonds, 342 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

  

> preset nih3d "ribbon by secondary structure (printable)"

Using preset: NIH3D / Ribbon by Secondary Structure (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.  
1710 atoms, 1368 bonds, 342 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 0 atom radii  
1364 atoms, 1358 bonds, 342 residues, 1 model selected  
189 hydrogen bonds found  
Changed 189 pseudobond radii  
Created 11 struts for @ca | ligand | P | ##num_atoms<500, max length 8, max
loop length 60  
  
Nothing selected  
Changed 2766 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|##num_atoms<500 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 monochrome"

Using preset: NIH3D / Ribbon Monochrome  
Changed 2688 atom radii, 2766 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.  
1710 atoms, 1368 bonds, 342 residues, 1 model selected  
Nothing selected  
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 "ribbon monochrome (printable)"

Using preset: NIH3D / Ribbon Monochrome (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.  
1710 atoms, 1368 bonds, 342 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 0 atom radii  
1364 atoms, 1358 bonds, 342 residues, 1 model selected  
189 hydrogen bonds found  
Changed 189 pseudobond radii  
Created 11 struts for @ca | ligand | P | ##num_atoms<500, max length 8, max
loop length 60  
  
Nothing selected  
Assigning color attribute to 200 items  
Changed 2766 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|##num_atoms<500 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 nih_blue
    setattr p color nih_blue
    size stickRadius 0.8
    style dashes 0

  

> preset nih3d "ribbon rainbow"

Using preset: NIH3D / Ribbon Rainbow  
Changed 2688 atom radii, 2766 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.  
1710 atoms, 1368 bonds, 342 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 @CA target r

  

> preset nih3d "ribbon rainbow (printable)"

Using preset: NIH3D / Ribbon Rainbow (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.  
1710 atoms, 1368 bonds, 342 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 0 atom radii  
1364 atoms, 1358 bonds, 342 residues, 1 model selected  
189 hydrogen bonds found  
Changed 189 pseudobond radii  
Created 11 struts for @ca | ligand | P | ##num_atoms<500, max length 8, max
loop length 60  
  
Nothing selected  
Changed 2766 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 @CA
    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|##num_atoms<500 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 2688 atom radii, 2766 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 2aph #1  
---  
notes | Termini for 2aph (#1) chain A determined from SEQRES records  
Termini for 2aph (#1) chain B determined from SEQRES records  
Termini for 2aph (#1) chain C determined from SEQRES records  
Termini for 2aph (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 177, /B VAL 177, /C
AMU 883, /D AMU 994  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 341, /B HIS 341, /C NH2
889, /D NH2 1000  
Chain-final residues that are not actual C termini:  
310 hydrogen bonds  
2590 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)
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 0.929429 sharp true
    rainbow #1@ca,c4' chains palette marine:goldenrod:firebrick:forest target rsa
    color zone #1 near #1 distance 20

  

> preset nih3d "surface by polymer"

Using preset: NIH3D / Surface by Polymer  
Changed 5278 atom radii, 5356 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 2aph #1  
---  
notes | Termini for 2aph (#1) chain A determined from SEQRES records  
Termini for 2aph (#1) chain B determined from SEQRES records  
Termini for 2aph (#1) chain C determined from SEQRES records  
Termini for 2aph (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 177, /B VAL 177, /C
AMU 883, /D AMU 994  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 341, /B HIS 341, /C NH2
889, /D NH2 1000  
Chain-final residues that are not actual C termini:  
293 hydrogen bonds  
0 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)
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 1.22247 sharp true
    color bypolymer target ar
    color zone #1 near #1 distance 20

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 5278 atom radii, 5356 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 2aph #1  
---  
notes | Termini for 2aph (#1) chain A determined from SEQRES records  
Termini for 2aph (#1) chain B determined from SEQRES records  
Termini for 2aph (#1) chain C determined from SEQRES records  
Termini for 2aph (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 177, /B VAL 177, /C
AMU 883, /D AMU 994  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 341, /B HIS 341, /C NH2
889, /D NH2 1000  
Chain-final residues that are not actual C termini:  
293 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue DAL+DAL (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpvnegzpsl\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpvnegzpsl\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n  
(DAL+DAL) ``  
(DAL+DAL) `Welcome to antechamber 20.0: molecular input file processor.`  
(DAL+DAL) ``  
(DAL+DAL) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpvnegzpsl\ante.in.mol2); atoms read
(29), bonds read (28).`  
(DAL+DAL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) ``  
(DAL+DAL) ``  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) `Info: Total number of electrons: 108; net charge: 0`  
(DAL+DAL) ``  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) ``  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) ``  
(DAL+DAL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(DAL+DAL) `bash.exe: warning: could not find /tmp, please create!`  
(DAL+DAL) ``  
Charges for residue DAL+DAL determined  
Assigning partial charges to residue AMU+ALA (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmp1listbnw\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmp1listbnw\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n  
(AMU+ALA) ``  
(AMU+ALA) `Welcome to antechamber 20.0: molecular input file processor.`  
(AMU+ALA) ``  
(AMU+ALA) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmp1listbnw\ante.in.mol2); atoms read
(53), bonds read (53).`  
(AMU+ALA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) ``  
(AMU+ALA) ``  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) `Info: Total number of electrons: 202; net charge: 0`  
(AMU+ALA) ``  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) ``  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) ``  
(AMU+ALA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(AMU+ALA) `bash.exe: warning: could not find /tmp, please create!`  
(AMU+ALA) ``  
Charges for residue AMU+ALA determined  
Assigning partial charges to residue GMA+LYS (net charge +1) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpng21xrrb\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpng21xrrb\ante.out.mol2 -fo mol2 -c
bcc -nc 1 -j 5 -s 2 -dr n  
(GMA+LYS) ``  
(GMA+LYS) `Welcome to antechamber 20.0: molecular input file processor.`  
(GMA+LYS) ``  
(GMA+LYS) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpng21xrrb\ante.in.mol2); atoms read
(51), bonds read (50).`  
(GMA+LYS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) ``  
(GMA+LYS) ``  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) `Info: Total number of electrons: 178; net charge: 1`  
(GMA+LYS) ``  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) ``  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) ``  
(GMA+LYS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(GMA+LYS) `bash.exe: warning: could not find /tmp, please create!`  
(GMA+LYS) ``  
Charges for residue GMA+LYS determined  
Coulombic values for Surface #1 #1.1: minimum, -13.24, mean -0.07, maximum
15.00  
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
    surface #1 enclose #1 grid 1.22247 sharp true
    color white
    coulombic surfaces #*

  

> preset nih3d "surface hydrophobicity"

Using preset: NIH3D / Surface Hydrophobicity  
Changed 5278 atom radii, 5356 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 2aph #1  
---  
notes | Termini for 2aph (#1) chain A determined from SEQRES records  
Termini for 2aph (#1) chain B determined from SEQRES records  
Termini for 2aph (#1) chain C determined from SEQRES records  
Termini for 2aph (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 177, /B VAL 177, /C
AMU 883, /D AMU 994  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 341, /B HIS 341, /C NH2
889, /D NH2 1000  
Chain-final residues that are not actual C termini:  
293 hydrogen bonds  
0 hydrogens added  
  
344 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)
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 1.22247 sharp true
    color magenta
    color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta

  

> preset nih3d "surface monochrome"

Using preset: NIH3D / Surface Monochrome  
Changed 5278 atom radii, 5356 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 2aph #1  
---  
notes | Termini for 2aph (#1) chain A determined from SEQRES records  
Termini for 2aph (#1) chain B determined from SEQRES records  
Termini for 2aph (#1) chain C determined from SEQRES records  
Termini for 2aph (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A VAL 177, /B VAL 177, /C
AMU 883, /D AMU 994  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 341, /B HIS 341, /C NH2
889, /D NH2 1000  
Chain-final residues that are not actual C termini:  
293 hydrogen bonds  
0 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)
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 1.22247 sharp true
    color nih_blue

  

> open pubchem:11006

Summary of feedback from opening 11006 fetched from pubchem  
---  
note | Fetching compressed PubChem 11006 from
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/11006/SDF?record_type=3d  
  
Number of charges (1) in PUBCHEM_MMFF94_PARTIAL_CHARGES data not equal to
number of atoms (50)  

> open "C:/Users/brownekm/Desktop/ChimeraX Bugs/1av7.pdb"

1av7.pdb title:  
Subtilisin carlsberg L-naphthyl-1-acetamido boronic acid inhibitor complex
[more info...]  
  
Chain information for 1av7.pdb #2  
---  
Chain | Description | UniProt  
A | subtilopeptidase A | SUBT_BACLI  
  
Non-standard residues in 1av7.pdb #2  
---  
NA — sodium ion  
  

> close session

> open "C:\Users\brownekm\Desktop\ChimeraX Bugs\1av7.pdb" format pdb

1av7.pdb title:  
Subtilisin carlsberg L-naphthyl-1-acetamido boronic acid inhibitor complex
[more info...]  
  
Chain information for 1av7.pdb #1  
---  
Chain | Description | UniProt  
A | subtilopeptidase A | SUBT_BACLI  
  
Non-standard residues in 1av7.pdb #1  
---  
NA — sodium ion  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 1968 atom radii, 1973 bond radii, 10 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 1av7.pdb #1  
---  
warning | Unknown hybridization for atom (B) of residue type SBL; not adding
hydrogens to it  
notes | Termini for 1av7.pdb (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 275  
Chain-final residues that are not actual C termini:  
237 hydrogen bonds  
1896 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue SBL (net charge +0) with am1-bcc method  
SBL: number of electrons (221) + formal charge (+0) is odd; cannot compute
charges for radical species using AM1-BCC method  




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
File attachment: 1av7.pdb

1av7.pdb​

[kristen.browne@…]

Added by email2trac

[pett]

Neither charge method (AM1-BCC, Gasteiger) can handle the boron in the SBL residue.

[kristen.browne@…]

Seems like this should probably be one that just fails the coulombic and moves to the next preset?  Phil?

K

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, November 15, 2022 2:05 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8035: Bad formal charge estimate

#8035: Bad formal charge estimate
----------------------------------------+----------------------
          Reporter:  kristen.browne@...   |      Owner:  pett
              Type:  defect             |     Status:  accepted
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------

Comment (by pett):

 Neither charge method (AM1-BCC, Gasteiger) can handle the boron in the SBL  residue.

--
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[pett]

The ChargeError does get caught by the command processing code, but that code then rethrows it as a UserError. I have changed the NIH3D script so that run_preset() catches UserError and issues a warning (instead of "crashing out"). I also changed it so that run_preset() returns a boolean as to whether it succeeded or not and the correspond output file only gets written if run_preset() succeeded. I have submitted a pull request with the changes.