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Opened 3 years ago
Closed 3 years ago
#8037 closed defect (limitation)
Charge-determination failure for CAS in 1fyw
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202210260016 (2022-10-26 00:16:05 UTC)
Description
open 1FYW
Failure running ANTECHAMBER for residue CAS
Maybe related to issue reported in #8028 which had a similar error
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
> close session
> open "C:/Users/brownekm/Downloads/a tRNA.pdb"
Chain information for a tRNA.pdb #1
---
Chain | Description
X | No description available
> 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.
2 atoms, 1 bond, 1 residue, 1 model selected
Nothing selected
Changed 0 pseudobond radii
Changed 0 atom radii
455 atoms, 454 bonds, 76 residues, 1 model selected
0 hydrogen bonds found
Changed 1 pseudobond radii
Created 4 struts for @ca | ligand | P | ##num_atoms<500, max length 8, max
loop length 60
Nothing selected
Changed 1818 bond radii
Changed 2 pseudobond dashes
Preset expands to these ChimeraX commands:
graphics bgcolor white
color name marine 0,50,100
color name forest 13.3,54.5,13.3
color name tangerine 95.3,51.8,0
color name grape 64.3,0,86.7
color name nih_blue 12.5,33.3,54.1
color name jmol_carbon 56.5,56.5,56.5
color name bond_purple 57.6,43.9,85.9
color name struts_grey 48,48,48
color name carbon_grey 22.2,22.2,22.2
surface close
preset 'initial styles' 'original look'
delete solvent
delete H
preset 'initial styles' cartoon
nucleotides ladder radius 1.2
color white target abc
color helix marine
color strand firebrick
color coil goldenrod
color nucleic-acid forest
color :A:C:G:U grape
color byatom
select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide)
color sel carbon_grey atoms
color ligand | protein & sideonly byhet atoms
~select
rainbow #1@ca,c4' chains palette marine:marine target rs
size min-backbone pseudobondRadius 1.1
size ions atomRadius +0.8
select backbone & protein | nucleic-acid & min-backbone | ions | ligand | ligand :< 5 & ~nucleic-acid
hbonds sel color white restrict both
size pseudobondRadius 0.6
wait 1
struts @ca|ligand|P|##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 coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 1629 atom radii, 1818 bond radii, 1 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 a tRNA.pdb #1
---
notes | No usable SEQRES records for a tRNA.pdb (#1) chain X; guessing termini
instead
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
105 hydrogen bonds
835 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /X VAL 77 H bonded to atom that should not have hydrogens (/X VAL 77
C)
> close session
> open "C:/Users/brownekm/Downloads/MolView (1)_2.mol"
PubChem entry 101561
> preset nih3d "ball and stick"
Using preset: NIH3D / Ball and Stick
Changed 16 atom radii, 15 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.
Changed 16 atom styles
Changed 8 atom radii
Changed 15 bond radii
Changed 1 ball scales
Changed 0 pseudobond radii
Changed 0 atom radii
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'
color jmol_carbon
color byhet
style ball
~nuc
~ribbon
disp
size H atomRadius 1.2
size stickRadius 0.24
size ballScale 0.3
size pseudobondRadius 0.3
size ions atomRadius +0.35
color pbonds bond_purple
> preset nih3d "ball and stick monochrome"
Using preset: NIH3D / Ball and Stick Monochrome
Changed 16 atom radii, 15 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.
Changed 16 atom styles
Changed 8 atom radii
Changed 15 bond radii
Changed 1 ball scales
Changed 0 pseudobond radii
Changed 0 atom radii
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'
color jmol_carbon
color byhet
style ball
~nuc
~ribbon
disp
size H atomRadius 1.2
size stickRadius 0.24
size ballScale 0.3
size pseudobondRadius 0.3
size ions atomRadius +0.35
color nih_blue
> preset nih3d cpk
Using preset: NIH3D / CPK
Changed 16 atom radii, 15 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.
Changed 16 atom styles
Changed 8 atom radii
Changed 0 atom radii
Changed 15 bond radii
Changed 0 pseudobond dashes
Changed 0 pseudobond radii
Changed 0 atom radii
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'
color jmol_carbon
color byhet
style sphere
~nuc
~ribbon
disp
size H atomRadius 1.1
size ions atomRadius +0.35
size stickRadius 0.8
style dashes 0
size pseudobondRadius 0.4
size ions atomRadius +0.35
> preset nih3d "cpk monochrome"
Using preset: NIH3D / CPK Monochrome
Changed 16 atom radii, 15 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.
Changed 16 atom styles
Changed 8 atom radii
Changed 0 atom radii
Changed 15 bond radii
Changed 0 pseudobond dashes
Changed 0 pseudobond radii
Changed 0 atom radii
Preset expands to these ChimeraX commands:
~struts
~hbonds
size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
style dashes 7
graphics bgcolor white
color name marine 0,50,100
color name forest 13.3,54.5,13.3
color name tangerine 95.3,51.8,0
color name grape 64.3,0,86.7
color name nih_blue 12.5,33.3,54.1
color name jmol_carbon 56.5,56.5,56.5
color name bond_purple 57.6,43.9,85.9
color name struts_grey 48,48,48
color name carbon_grey 22.2,22.2,22.2
surface close
preset 'initial styles' 'original look'
style sphere
~nuc
~ribbon
disp
color nih_blue
size H atomRadius 1.1
size ions atomRadius +0.35
size stickRadius 0.8
style dashes 0
size pseudobondRadius 0.4
size ions atomRadius +0.35
> preset nih3d sticks
Using preset: NIH3D / Sticks
Changed 16 atom radii, 15 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.
Changed 16 atom styles
Preset expands to these ChimeraX commands:
~struts
~hbonds
size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
style dashes 7
graphics bgcolor white
color name marine 0,50,100
color name forest 13.3,54.5,13.3
color name tangerine 95.3,51.8,0
color name grape 64.3,0,86.7
color name nih_blue 12.5,33.3,54.1
color name jmol_carbon 56.5,56.5,56.5
color name bond_purple 57.6,43.9,85.9
color name struts_grey 48,48,48
color name carbon_grey 22.2,22.2,22.2
surface close
preset 'initial styles' 'original look'
color jmol_carbon
color byhet
style stick
~nuc
~ribbon
disp
> preset nih3d "sticks (printable)"
Using preset: NIH3D / Sticks (Printable)
Changed 16 atom radii, 15 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.
Changed 16 atom styles
Changed 15 bond radii
Changed 0 pseudobond dashes
Changed 0 pseudobond radii
Changed 0 atom radii
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'
color jmol_carbon
color byhet
style stick
~nuc
~ribbon
disp
size stickRadius 0.8
style dashes 0
size pseudobondRadius 0.4
size ions atomRadius +0.35
> preset nih3d "sticks monochrome (printable)"
Using preset: NIH3D / Sticks Monochrome (Printable)
Changed 16 atom radii, 15 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.
Changed 16 atom styles
Changed 15 bond radii
Changed 0 pseudobond dashes
Changed 0 pseudobond radii
Changed 0 atom radii
Preset expands to these ChimeraX commands:
~struts
~hbonds
size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
style dashes 7
graphics bgcolor white
color name marine 0,50,100
color name forest 13.3,54.5,13.3
color name tangerine 95.3,51.8,0
color name grape 64.3,0,86.7
color name nih_blue 12.5,33.3,54.1
color name jmol_carbon 56.5,56.5,56.5
color name bond_purple 57.6,43.9,85.9
color name struts_grey 48,48,48
color name carbon_grey 22.2,22.2,22.2
surface close
preset 'initial styles' 'original look'
style stick
~nuc
~ribbon
disp
color nih_blue
size stickRadius 0.8
style dashes 0
size pseudobondRadius 0.4
size ions atomRadius +0.35
> close session
> open pubchem:94213
Summary of feedback from opening 94213 fetched from pubchem
---
note | Fetching compressed PubChem 94213 from
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/94213/SDF?record_type=3d
Number of charges (1) in PUBCHEM_MMFF94_PARTIAL_CHARGES data not equal to
number of atoms (38)
> open pubchem:24526
Summary of feedback from opening 24526 fetched from pubchem
---
note | Fetching compressed PubChem 24526 from
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/24526/SDF?record_type=3d
Number of charges (1) in PUBCHEM_MMFF94_PARTIAL_CHARGES data not equal to
number of atoms (2)
> open pubchem:6556
Summary of feedback from opening 6556 fetched from pubchem
---
note | Fetching compressed PubChem 6556 from
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6556/SDF?record_type=3d
Number of charges (1) in PUBCHEM_MMFF94_PARTIAL_CHARGES data not equal to
number of atoms (17)
> open C:/Users/brownekm/Downloads/4djh_modified.pdb
Summary of feedback from opening C:/Users/brownekm/Downloads/4djh_modified.pdb
---
warnings | CONECT record to nonexistent atom: (1602, 1604)
CONECT record for nonexistent atom: 1604
Start residue of secondary structure not found: HELIX 9 9 ASN A 1002 GLU A
1011 1 10
Start residue of secondary structure not found: HELIX 10 10 SER A 1038 GLY A
1051 1 14
Start residue of secondary structure not found: HELIX 11 11 THR A 1059 ASN A
1081 1 23
Start residue of secondary structure not found: HELIX 12 12 LYS A 1083 LEU A
1091 1 9
Start residue of secondary structure not found: HELIX 13 13 ASP A 1092 GLY A
1113 1 22
35 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue ASN (1002 )
Cannot find LINK/SSBOND residue TYR (1161 )
Cannot find LINK/SSBOND residue GLY (261 )
Cannot find LINK/SSBOND residue TYR (1161 )
4djh_modified.pdb title:
Structure of the human κ opioid receptor In complex with jdtic [more info...]
Chain information for 4djh_modified.pdb #1
---
Chain | Description | UniProt
A | κ-type opioid receptor, lysozyme | OPRK_HUMAN
Non-standard residues in 4djh_modified.pdb #1
---
JDC —
(3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 2258 atom radii, 2314 bond radii, 3 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 4djh_modified.pdb #1
---
warnings | Not adding hydrogens to /A ILE 85 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A THR 88 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 89 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 165 CE because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 167 CB because it is missing heavy-atom bond
partners
13 messages similar to the above omitted
notes | Termini for 4djh_modified.pdb (#1) chain A determined from SEQRES
records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A SER 55, /A ARG 263,
/A ALA 307
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A GLY 261, /A SER 301, /A
PRO 347
274 hydrogen bonds
Adding 'H' to /A SER 55
Adding 'H' to /A ARG 263
Adding 'H' to /A ALA 307
/A PRO 347 is not terminus, removing H atom from 'C'
2286 hydrogens added
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ILE 85
/A THR 88
/A LYS 89
/A LYS 165
/A LEU 167
/A PHE 169
/A LYS 200
/A ASP 217
/A ARG 257
/A LEU 259
/A LYS 265
/A ARG 267
/A ARG 270
/A ARG 271
/A VAL 296
/A SER 301
/A GLU 335
/A ARG 342
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /A SER 260 H bonded to atom that should not have hydrogens (/A SER
260 C)
> open 1W5U
Summary of feedback from opening 1W5U fetched from pdb
---
warnings | Ignoring microheterogeneity for label_seq_id 11 in chain B
Ignoring microheterogeneity for label_seq_id 11 in chain D
notes | Fetching compressed mmCIF 1w5u from
http://files.rcsb.org/download/1w5u.cif
Fetching CCD FVA from http://ligand-expo.rcsb.org/reports/F/FVA/FVA.cif
Fetching CCD DLE from http://ligand-expo.rcsb.org/reports/D/DLE/DLE.cif
Fetching CCD DVA from http://ligand-expo.rcsb.org/reports/D/DVA/DVA.cif
Fetching CCD ETA from http://ligand-expo.rcsb.org/reports/E/ETA/ETA.cif
Fetching CCD RB from http://ligand-expo.rcsb.org/reports/R/RB/RB.cif
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif
Fetching CCD EOH from http://ligand-expo.rcsb.org/reports/E/EOH/EOH.cif
1w5u title:
Gramicidin D from bacillus brevis (ethanol solvate) [more info...]
Chain information for 1w5u #2
---
Chain | Description
A B C D | GRAMICIDIN D
Non-standard residues in 1w5u #2
---
CL — chloride ion
EOH — ethanol
ETA — ethanolamine
RB — rubidium ion
1w5u mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> close session
> open 1W5U format mmcif fromDatabase pdb
Summary of feedback from opening 1W5U fetched from pdb
---
warnings | Ignoring microheterogeneity for label_seq_id 11 in chain B
Ignoring microheterogeneity for label_seq_id 11 in chain D
1w5u title:
Gramicidin D from bacillus brevis (ethanol solvate) [more info...]
Chain information for 1w5u #1
---
Chain | Description
A B C D | GRAMICIDIN D
Non-standard residues in 1w5u #1
---
CL — chloride ion
EOH — ethanol
ETA — ethanolamine
RB — rubidium ion
1w5u mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 597 atom radii, 573 bond radii, 19 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 1w5u #1
---
notes | Termini for 1w5u (#1) chain A determined from SEQRES records
Termini for 1w5u (#1) chain B determined from SEQRES records
Termini for 1w5u (#1) chain C determined from SEQRES records
Termini for 1w5u (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /A FVA 1, /B FVA 1, /C FVA
1, /D FVA 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ETA 16, /B ETA 16, /C ETA
16, /D ETA 16
Chain-final residues that are not actual C termini:
56 hydrogen bonds
566 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue DLE (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\tmpkc2s6l_p\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpkc2s6l_p\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(DLE) ``
(DLE) `Welcome to antechamber 20.0: molecular input file processor.`
(DLE) ``
(DLE) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpkc2s6l_p\ante.in.mol2); atoms read
(31), bonds read (30).`
(DLE) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(DLE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(DLE) `bash.exe: warning: could not find /tmp, please create!`
(DLE) ``
(DLE) ``
(DLE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(DLE) `bash.exe: warning: could not find /tmp, please create!`
(DLE) `Info: Total number of electrons: 102; net charge: 0`
(DLE) ``
(DLE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(DLE) `bash.exe: warning: could not find /tmp, please create!`
(DLE) ``
(DLE) `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`
(DLE) `bash.exe: warning: could not find /tmp, please create!`
(DLE) ``
(DLE) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(DLE) `bash.exe: warning: could not find /tmp, please create!`
(DLE) ``
Charges for residue DLE determined
Assigning partial charges to residue DVA (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\tmppixuq4ib\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmppixuq4ib\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(DVA) ``
(DVA) `Welcome to antechamber 20.0: molecular input file processor.`
(DVA) ``
(DVA) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmppixuq4ib\ante.in.mol2); atoms read
(28), bonds read (27).`
(DVA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(DVA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(DVA) `bash.exe: warning: could not find /tmp, please create!`
(DVA) ``
(DVA) ``
(DVA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(DVA) `bash.exe: warning: could not find /tmp, please create!`
(DVA) `Info: Total number of electrons: 94; net charge: 0`
(DVA) ``
(DVA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(DVA) `bash.exe: warning: could not find /tmp, please create!`
(DVA) ``
(DVA) `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`
(DVA) `bash.exe: warning: could not find /tmp, please create!`
(DVA) ``
(DVA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(DVA) `bash.exe: warning: could not find /tmp, please create!`
(DVA) ``
Charges for residue DVA determined
Assigning partial charges to residue FVA (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\tmpzv3n9nv4\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpzv3n9nv4\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(FVA) ``
(FVA) `Welcome to antechamber 20.0: molecular input file processor.`
(FVA) ``
(FVA) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpzv3n9nv4\ante.in.mol2); atoms read
(25), bonds read (24).`
(FVA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(FVA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(FVA) `bash.exe: warning: could not find /tmp, please create!`
(FVA) ``
(FVA) ``
(FVA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(FVA) `bash.exe: warning: could not find /tmp, please create!`
(FVA) `Info: Total number of electrons: 86; net charge: 0`
(FVA) ``
(FVA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(FVA) `bash.exe: warning: could not find /tmp, please create!`
(FVA) ``
(FVA) `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`
(FVA) `bash.exe: warning: could not find /tmp, please create!`
(FVA) ``
(FVA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(FVA) `bash.exe: warning: could not find /tmp, please create!`
(FVA) ``
Charges for residue FVA determined
Assigning partial charges to residue ETA (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\tmp75jus6e3\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmp75jus6e3\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(ETA) ``
(ETA) `Welcome to antechamber 20.0: molecular input file processor.`
(ETA) ``
(ETA) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmp75jus6e3\ante.in.mol2); atoms read
(16), bonds read (15).`
(ETA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(ETA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) ``
(ETA) ``
(ETA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) `Info: Total number of electrons: 56; net charge: 0`
(ETA) ``
(ETA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) ``
(ETA) `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`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) ``
(ETA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) ``
Charges for residue ETA determined
Assigning partial charges to residue ETA (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\tmpic0nmkuf\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpic0nmkuf\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(ETA) ``
(ETA) `Welcome to antechamber 20.0: molecular input file processor.`
(ETA) ``
(ETA) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpic0nmkuf\ante.in.mol2); atoms read
(15), bonds read (14).`
(ETA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(ETA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) ``
(ETA) ``
(ETA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) `Info: Total number of electrons: 48; net charge: 0`
(ETA) ``
(ETA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) ``
(ETA) `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`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) ``
(ETA) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(ETA) `bash.exe: warning: could not find /tmp, please create!`
(ETA) ``
Charges for residue ETA determined
Coulombic values for Surface #1 #1.2: minimum, -7.06, mean -0.19, maximum 6.11
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 0.5 sharp true
color white
coulombic surfaces #*
> preset nih3d "surface hydrophobicity"
Using preset: NIH3D / Surface Hydrophobicity
Changed 1132 atom radii, 1139 bond radii, 7 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 1w5u #1
---
notes | Termini for 1w5u (#1) chain A determined from SEQRES records
Termini for 1w5u (#1) chain B determined from SEQRES records
Termini for 1w5u (#1) chain C determined from SEQRES records
Termini for 1w5u (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /A FVA 1, /B FVA 1, /C FVA
1, /D FVA 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ETA 16, /B ETA 16, /C ETA
16, /D ETA 16
Chain-final residues that are not actual C termini:
54 hydrogen bonds
0 hydrogens added
64 residues, 1 surfaces, atom kd_hydrophobicity range -0.9 to 4.2
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 0.553846 sharp true
color magenta
color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta
> preset nih3d "surface hydrophobicity"
Using preset: NIH3D / Surface Hydrophobicity
Changed 1118 atom radii, 1139 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 1w5u #1
---
notes | Termini for 1w5u (#1) chain A determined from SEQRES records
Termini for 1w5u (#1) chain B determined from SEQRES records
Termini for 1w5u (#1) chain C determined from SEQRES records
Termini for 1w5u (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /A FVA 1, /B FVA 1, /C FVA
1, /D FVA 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ETA 16, /B ETA 16, /C ETA
16, /D ETA 16
Chain-final residues that are not actual C termini:
54 hydrogen bonds
0 hydrogens added
64 residues, 1 surfaces, atom kd_hydrophobicity range -0.9 to 4.2
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 0.548442 sharp true
color magenta
color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 1118 atom radii, 1139 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 1w5u #1
---
notes | Termini for 1w5u (#1) chain A determined from SEQRES records
Termini for 1w5u (#1) chain B determined from SEQRES records
Termini for 1w5u (#1) chain C determined from SEQRES records
Termini for 1w5u (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /A FVA 1, /B FVA 1, /C FVA
1, /D FVA 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ETA 16, /B ETA 16, /C ETA
16, /D ETA 16
Chain-final residues that are not actual C termini:
54 hydrogen bonds
0 hydrogens added
Coulombic values for Surface #1 #1.2: minimum, -6.87, mean -0.02, maximum 5.87
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 0.548442 sharp true
color white
coulombic surfaces #*
> open 2APH
2aph title:
Crystal structure of human PGRP-IalphaC in complex with muramyl pentapeptide
[more info...]
Chain information for 2aph #2
---
Chain | Description | UniProt
A B | Peptidoglycan recognition protein I-alpha | PGRP3_HUMAN
C D | muramyl pentapeptide |
Non-standard residues in 2aph #2
---
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
> close session
> 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
2 tautomers of DAL+DAL; charging separately
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmp7g3idzv2\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmp7g3idzv2\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\tmp7g3idzv2\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
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpla2jvxir\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpla2jvxir\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\tmpla2jvxir\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\tmp599ted0o\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmp599ted0o\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\tmp599ted0o\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\tmpfwf3d_y_\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpfwf3d_y_\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\tmpfwf3d_y_\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
23.16
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 #*
> open pubchem: 10037
'10037' has no suffix
> open pubchem:10037
Fetching url
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/10037/SDF?record_type=3d
failed:
HTTP Error 404: PUGREST.NotFound
> close session
> open C:/Users/brownekm/Downloads/1n26-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/h-Orai1-Dong_state01.pdb
Chain information for h-Orai1-Dong_state01.pdb #1
---
Chain | Description
P | No description available
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 20775 atom radii, 21021 bond radii, 2 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 h-Orai1-Dong_state01.pdb #1
---
warnings | Not adding hydrogens to /P THR 295 C because it is missing heavy-
atom bond partners
Not adding hydrogens to /P THR 295 C because it is missing heavy-atom bond
partners
Unknown hybridization for atoms (OT2, OT1) of residue type THR; not adding
hydrogens to them
notes | No usable SEQRES records for h-Orai1-Dong_state01.pdb (#1) chain P;
guessing termini instead
Chain-initial residues that are actual N termini: /P GLN 72
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /P HSE 288
1139 hydrogen bonds
/P HSE 288 is not terminus, removing H atom from 'C'
13 hydrogens added
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/P ILE 121
/P ILE 121
/P ILE 121
/P ILE 121
/P ILE 121
/P ILE 121
/P ILE 140
/P ILE 140
/P ILE 140
/P ILE 140
/P ILE 140
/P ILE 140
/P ILE 144
/P ILE 144
/P ILE 144
/P ILE 144
/P ILE 144
/P ILE 144
/P ILE 148
/P ILE 148
/P ILE 148
/P ILE 148
/P ILE 148
/P ILE 148
/P ILE 172
/P ILE 172
/P ILE 172
/P ILE 172
/P ILE 172
/P ILE 172
/P ILE 182
/P ILE 182
/P ILE 182
/P ILE 182
/P ILE 182
/P ILE 182
/P ILE 229
/P ILE 229
/P ILE 229
/P ILE 229
/P ILE 229
/P ILE 229
/P ILE 237
/P ILE 237
/P ILE 237
/P ILE 237
/P ILE 237
/P ILE 237
/P ILE 242
/P ILE 242
/P ILE 242
/P ILE 242
/P ILE 242
/P ILE 242
/P ILE 249
/P ILE 249
/P ILE 249
/P ILE 249
/P ILE 249
/P ILE 249
/P ILE 251
/P ILE 251
/P ILE 251
/P ILE 251
/P ILE 251
/P ILE 251
/P ARG 289
/P ARG 289
/P THR 295
/P THR 295
/P THR 295
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /P CYS 195 HG1 bonded to atom that should not have hydrogens (/P CYS
195 SG)
> close session
> open "C:/Users/brownekm/Downloads/d-Orai1-Dong_state01 (1).pdb"
Chain information for d-Orai1-Dong_state01 (1).pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 18381 atom radii, 18600 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 d-Orai1-Dong_state01 (1).pdb #1
---
warnings | Both O and OXT missing from C-terminal residue /A HSE 334; cannot
complete teminus
Both O and OXT missing from C-terminal residue /B ASP 329; cannot complete
teminus
Both O and OXT missing from C-terminal residue /C HSE 334; cannot complete
teminus
Both O and OXT missing from C-terminal residue /D ASP 329; cannot complete
teminus
Both O and OXT missing from C-terminal residue /E HSE 334; cannot complete
teminus
1 messages similar to the above omitted
notes | No usable SEQRES records for d-Orai1-Dong_state01 (1).pdb (#1) chain
A; guessing termini instead
No usable SEQRES records for d-Orai1-Dong_state01 (1).pdb (#1) chain B;
guessing termini instead
No usable SEQRES records for d-Orai1-Dong_state01 (1).pdb (#1) chain C;
guessing termini instead
No usable SEQRES records for d-Orai1-Dong_state01 (1).pdb (#1) chain D;
guessing termini instead
No usable SEQRES records for d-Orai1-Dong_state01 (1).pdb (#1) chain E;
guessing termini instead
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A THR 144, /B THR 144, /C
THR 144, /D THR 144, /E THR 144, /F THR 144
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A HSE 334, /B ASP 329, /C HSE
334, /D ASP 329, /E HSE 334, /F ASP 329
Chain-final residues that are not actual C termini:
1066 hydrogen bonds
0 hydrogens added
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ILE 193
/A ILE 197
/A ILE 212
/A ILE 216
/A ILE 220
/A ILE 229
/A ILE 244
/A ILE 257
/A ILE 263
/A ILE 265
/A ILE 287
/A ILE 291
/A ILE 292
/A ILE 298
/A ILE 316
/B ILE 193
/B ILE 197
/B ILE 212
/B ILE 216
/B ILE 220
/B ILE 229
/B ILE 244
/B ILE 257
/B ILE 263
/B ILE 265
/B ILE 287
/B ILE 291
/B ILE 292
/B ILE 298
/B ILE 316
/B ASP 329
/C ILE 193
/C ILE 197
/C ILE 212
/C ILE 216
/C ILE 220
/C ILE 229
/C ILE 244
/C ILE 257
/C ILE 263
/C ILE 265
/C ILE 287
/C ILE 291
/C ILE 292
/C ILE 298
/C ILE 316
/D ILE 193
/D ILE 197
/D ILE 212
/D ILE 216
/D ILE 220
/D ILE 229
/D ILE 244
/D ILE 257
/D ILE 263
/D ILE 265
/D ILE 287
/D ILE 291
/D ILE 292
/D ILE 298
/D ILE 316
/D ASP 329
/E ILE 193
/E ILE 197
/E ILE 212
/E ILE 216
/E ILE 220
/E ILE 229
/E ILE 244
/E ILE 257
/E ILE 263
/E ILE 265
/E ILE 287
/E ILE 291
/E ILE 292
/E ILE 298
/E ILE 316
/F ILE 193
/F ILE 197
/F ILE 212
/F ILE 216
/F ILE 220
/F ILE 229
/F ILE 244
/F ILE 257
/F ILE 263
/F ILE 265
/F ILE 287
/F ILE 291
/F ILE 292
/F ILE 298
/F ILE 316
/F ASP 329
Using Amber 20 recommended default charges and atom types for standard
residues
Nonstandard name for heavy atom /F ILE 229 CD
> close session
> open C:/Users/brownekm/Downloads/1saf-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/ago_TRPML1_PS.pdb
Chain information for ago_TRPML1_PS.pdb #1
---
Chain | Description
A B C D | No description available
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 15544 atom radii, 15960 bond radii, 4 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 ago_TRPML1_PS.pdb #1
---
notes | No usable SEQRES records for ago_TRPML1_PS.pdb (#1) chain A; guessing
termini instead
No usable SEQRES records for ago_TRPML1_PS.pdb (#1) chain B; guessing termini
instead
No usable SEQRES records for ago_TRPML1_PS.pdb (#1) chain C; guessing termini
instead
No usable SEQRES records for ago_TRPML1_PS.pdb (#1) chain D; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLU 38, /B GLU 38, /C GLU
38, /D GLU 38
Chain-initial residues that are not actual N termini: /A SER 216, /B SER 216,
/C SER 216, /D SER 216
Chain-final residues that are actual C termini: /A HIS 526, /B HIS 526, /C HIS
526, /D HIS 526
Chain-final residues that are not actual C termini: /A PRO 205, /B PRO 205, /C
PRO 205, /D PRO 205
1484 hydrogen bonds
Adding 'H' to /A SER 216
Adding 'H' to /B SER 216
Adding 'H' to /C SER 216
Adding 'H' to /D SER 216
15648 hydrogens added
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ILE 81
/A ILE 99
/A ILE 129
/A ILE 193
/A ILE 233
/A ILE 240
/A ILE 246
/A ILE 260
/A ILE 271
/A ILE 273
/A ILE 281
/A ILE 306
/A ILE 435
/A ILE 445
/A ILE 468
/A ILE 502
/A ILE 514
/A ILE 517
/A ILE 524
/B ILE 81
/B ILE 99
/B ILE 129
/B ILE 193
/B ILE 233
/B ILE 240
/B ILE 246
/B ILE 260
/B ILE 271
/B ILE 273
/B ILE 281
/B ILE 306
/B ILE 388
/B ILE 435
/B ILE 445
/B ILE 468
/B ILE 502
/B ILE 514
/B ILE 517
/B ILE 524
/C ILE 73
/C ILE 81
/C ILE 99
/C ILE 129
/C ILE 184
/C ILE 193
/C ILE 233
/C ILE 240
/C ILE 246
/C ILE 260
/C ILE 271
/C ILE 273
/C ILE 281
/C ILE 306
/C ILE 388
/C ILE 435
/C ILE 445
/C ILE 468
/C ILE 502
/C ILE 514
/C ILE 517
/C ILE 524
/D ILE 81
/D ILE 99
/D ILE 129
/D ILE 184
/D ILE 193
/D ILE 233
/D ILE 246
/D ILE 260
/D ILE 271
/D ILE 273
/D ILE 281
/D ILE 306
/D ILE 388
/D ILE 435
/D ILE 445
/D ILE 468
/D ILE 502
/D ILE 514
/D ILE 517
/D ILE 524
Using Amber 20 recommended default charges and atom types for standard
residues
Nonstandard name for heavy atom /D ILE 260 CD
> close session
> open C:/Users/brownekm/Downloads/1eaa-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/1eaa-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/1igt-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/1igt-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/3fsn-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/5f5m-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/5dvw-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/2w50-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/3fke-assembly-1_0.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/4m0q-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/4obe-assembly-1_0.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/4plu-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/2fae-assembly-1.cif
mmCIF parsing error: unexpected data value near line 1
> open C:/Users/brownekm/Downloads/5MSG_model-annotate_P1.pdb
5MSG_model-annotate_P1.pdb title:
Influenza B polymerase bound to VRNA promoter and capped RNA primer [more
info...]
Chain information for 5MSG_model-annotate_P1.pdb #1
---
Chain | Description | UniProt
A | polymerase acidic protein | Q5V8Z9_9INFB
B | RNA-directed RNA polymerase catalytic subunit | Q5V8Y6_9INFB
C | polymerase basic protein 2 | Q5V8X3_9INFB
M | RNA (5'-D(*(GDM))-R(P*ap*ap*up*C)-3') |
R | RNA (5'- R(*up*ap*up*ap*CP*CP*up*CP*up*GP*CP*up*up*CP*up*GP*CP*U)-3') |
V | RNA (5'-R(P*ap*GP*up*ap*GP*up*ap*ap*CP*ap*ap*GP*ap*G)-3') |
Non-standard residues in 5MSG_model-annotate_P1.pdb #1
---
M7G — 7N-methyl-8-hydroguanosine-5'-diphosphate
PO4 — phosphate ion
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 18236 atom radii, 18650 bond radii, 3 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 5MSG_model-annotate_P1.pdb #1
---
warning | Not adding hydrogens to /R U 1 C4' because it is missing heavy-atom
bond partners
notes | Termini for 5MSG_model-annotate_P1.pdb (#1) chain A determined from
SEQRES records
Termini for 5MSG_model-annotate_P1.pdb (#1) chain B determined from SEQRES
records
Termini for 5MSG_model-annotate_P1.pdb (#1) chain C determined from SEQRES
records
Termini for 5MSG_model-annotate_P1.pdb (#1) chain M determined from SEQRES
records
Termini for 5MSG_model-annotate_P1.pdb (#1) chain R determined from SEQRES
records
1 messages similar to the above omitted
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A SER 0, /A GLN 71, /B
GLY 0, /B PRO 650, /C GLY 0, /C LYS 496
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A ALA 63, /A ILE 723, /B
THR 645, /B ILE 749, /C VAL 485, /C LYS 740
Chain-initial residues that are not actual 5' termini: /M A 1
2014 hydrogen bonds
Adding 'H' to /A SER 0
Adding 'H' to /A GLN 71
Adding 'H' to /B GLY 0
Adding 'H' to /C GLY 0
Adding 'H' to /C LYS 496
/A ILE 723 is not terminus, removing H atom from 'C'
/B ILE 749 is not terminus, removing H atom from 'C'
/C LYS 740 is not terminus, removing H atom from 'C'
/M C 4 is not terminus, removing H atom from O3'
18016 hydrogens added
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/R U 1
/R U 18
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /R U 18 H5' bonded to atom that should not have hydrogens (/R U 18
O5')
> open 1FYW
Summary of feedback from opening 1FYW fetched from pdb
---
notes | Fetching compressed mmCIF 1fyw from
http://files.rcsb.org/download/1fyw.cif
Fetching CCD CAS from http://ligand-expo.rcsb.org/reports/C/CAS/CAS.cif
1fyw title:
Crystal structure of the tir domain of human TLR2 [more info...]
Chain information for 1fyw #2
---
Chain | Description | UniProt
A | TOLL-LIKE RECEPTOR 2 | TLR2_HUMAN
1fyw mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> close session
> open 1FYW format mmcif fromDatabase pdb
1fyw title:
Crystal structure of the tir domain of human TLR2 [more info...]
Chain information for 1fyw #1
---
Chain | Description | UniProt
A | TOLL-LIKE RECEPTOR 2 | TLR2_HUMAN
1fyw mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 1266 atom radii, 1300 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 1fyw #1
---
warnings | Unknown hybridization for atom (AS) of residue type CAS; not adding
hydrogens to it
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it
notes | Termini for 1fyw (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini: /A SER 636
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A SER 784
Chain-final residues that are not actual C termini:
118 hydrogen bonds
1240 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CAS (net charge +0) with am1-bcc method
Atom whose IDATM type has no equivalent Sybyl type: /? CAS 1 As1 (type: As)
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpvju_heqe\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpvju_heqe\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(CAS) ``
(CAS) `Welcome to antechamber 20.0: molecular input file processor.`
(CAS) ``
(CAS) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpvju_heqe\ante.in.mol2); atoms read
(23), bonds read (22).`
(CAS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CAS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `Warning: For atom (ID: 7, Name: As1) the best APS is not zero.`
(CAS) ` Bonds involving this atom are frozen.`
(CAS) ``
(CAS) ``
(CAS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `Info: Total number of electrons: 126; net charge: 0`
(CAS) ``
(CAS) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(CAS) `bash.exe: warning: could not find /tmp, please create!`
(CAS) `/usr/bin/antechamber: Fatal Error!`
(CAS) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`
Failure running ANTECHAMBER for residue CAS
Check reply log for details
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
Change History (2)
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 → Charge-determination failure for CAS in 1fyw |
comment:2 by , 3 years ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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Neither charge-determination method can handle the arsenic in the CAS residue, so the coulombic preset will be skipped in the latest version of the pipeline script.