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Opened 3 years ago
Closed 3 years ago
#8035 closed defect (limitation)
Bad formal charge estimate
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | phil.cruz@…, 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.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
Attachments (1)
Change History (5)
by , 3 years ago
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Bad formal charge estimate |
comment:2 by , 3 years ago
Neither charge method (AM1-BCC, Gasteiger) can handle the boron in the SBL residue.
comment:3 by , 3 years ago
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.
--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8035%23comment%3A2&data=05%7C01%7Ckristen.browne%40nih.gov%7Ce070b7863c9a428308f508dac73c541b%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638041359167242510%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SK2nVA5xqt2gpjacoS%2BUNdKibUsaRtCBQKB7x7cGK64%3D&reserved=0>
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follow-up: 3 comment:4 by , 3 years ago
| Cc: | added |
|---|---|
| Resolution: | → limitation |
| Status: | accepted → closed |
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.
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