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Opened 3 years ago
Closed 3 years ago
#8073 closed defect (limitation)
Could not come up with unique atom name in mega-residue
| 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
open 4R8I
Had a similar error before with mol2 file that was fixed in ticket:
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8022
Might not be fixable and need to just skip Coulombic, but thought I'd check.
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 3OE0
Summary of feedback from opening 3OE0 fetched from pdb
---
notes | Fetching compressed mmCIF 3oe0 from
http://files.rcsb.org/download/3oe0.cif
Fetching CCD ALN from http://ligand-expo.rcsb.org/reports/A/ALN/ALN.cif
Fetching CCD DPR from http://ligand-expo.rcsb.org/reports/D/DPR/DPR.cif
Fetching CCD CIR from http://ligand-expo.rcsb.org/reports/C/CIR/CIR.cif
3oe0 title:
Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic
peptide antagonist CVX15 [more info...]
Chain information for 3oe0 #1
---
Chain | Description | UniProt
A | C-X-C chemokine receptor type 4, Lysozyme Chimera | CXCR4_HUMAN
I | Polyphemusin analog, CXC chemokine receptor antagonist |
3oe0 mmCIF Assemblies
---
1| author_defined_assembly
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 3640 atom radii, 3728 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 3oe0 #1
---
warnings | Not adding hydrogens to /A GLN 233 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A LYS 234 CB because it is missing heavy-atom bond
partners
notes | Termini for 3oe0 (#1) chain A determined from SEQRES records
Termini for 3oe0 (#1) chain I determined from SEQRES records
Chain-initial residues that are actual N termini: /I ARG 1
Chain-initial residues that are not actual N termini: /A LYS 25, /A SER 71, /A
GLY 231
Chain-final residues that are actual C termini: /I DPR 16
Chain-final residues that are not actual C termini: /A GLN 66, /A TYR 1161, /A
ALA 303
436 hydrogen bonds
Adding 'H' to /A LYS 25
Adding 'H' to /A SER 71
Adding 'H' to /A GLY 231
/A ALA 303 is not terminus, removing H atom from 'C'
3686 hydrogens added
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A LYS 234 CD
/A LYS 234 CE
/A LYS 234 CG
/A LYS 234 NZ
/A GLN 233 CD
/A GLN 233 CG
/A GLN 233 OE1
/A GLN 233 NE2
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue ALN (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.4/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmp__qs84dv\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmp__qs84dv\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(ALN) ``
(ALN) `Welcome to antechamber 20.0: molecular input file processor.`
(ALN) ``
(ALN) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmp__qs84dv\ante.in.mol2); atoms read
(38), bonds read (39).`
(ALN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(ALN) `bash.exe: warning: could not find /tmp, please create!`
(ALN) ``
(ALN) ``
(ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(ALN) `bash.exe: warning: could not find /tmp, please create!`
(ALN) `Info: Total number of electrons: 144; net charge: 0`
(ALN) ``
(ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`
(ALN) `bash.exe: warning: could not find /tmp, please create!`
(ALN) ``
(ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.4/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(ALN) `bash.exe: warning: could not find /tmp, please create!`
(ALN) ``
(ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(ALN) `bash.exe: warning: could not find /tmp, please create!`
(ALN) ``
Charges for residue ALN determined
Assigning partial charges to residue CIR+ARG+CYS (net charge +2) with am1-bcc
method
CIR+ARG+CYS: number of electrons (287) + formal charge (+2) is odd; cannot
compute charges for radical species using AM1-BCC method
> close session
> open 5BT0
Summary of feedback from opening 5BT0 fetched from pdb
---
notes | Fetching compressed mmCIF 5bt0 from
http://files.rcsb.org/download/5bt0.cif
Fetching CCD CRO from http://ligand-expo.rcsb.org/reports/C/CRO/CRO.cif
Fetching CCD HOX from http://ligand-expo.rcsb.org/reports/H/HOX/HOX.cif
5bt0 title:
Switching GFP fluorescence using genetically encoded phenyl azide chemistry
through two different non-native post-translational modifications routes at
the same position. [more info...]
Chain information for 5bt0 #1
---
Chain | Description | UniProt
A B | Green fluorescent protein | A0A059PIQ0_AEQVI
Non-standard residues in 5bt0 #1
---
CRO —
{2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (peptide derived chromophore)
SO4 — sulfate ion
5bt0 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 4055 atom radii, 3788 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 5bt0 #1
---
warning | Not adding hydrogens to /A GLU 142 CB because it is missing heavy-
atom bond partners
notes | Termini for 5bt0 (#1) chain A determined from SEQRES records
Termini for 5bt0 (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A SER 2, /B SER 2
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASP 234, /B ASP 234
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A ASP 234
Missing OXT added to C-terminal residue /B ASP 234
445 hydrogen bonds
3594 hydrogens added
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A GLU 142 CD
/A GLU 142 OE2
/A GLU 142 CG
/A GLU 142 OE1
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HOX (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.4/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmp4jrgi1ju\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmp4jrgi1ju\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(HOX) ``
(HOX) `Welcome to antechamber 20.0: molecular input file processor.`
(HOX) ``
(HOX) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmp4jrgi1ju\ante.in.mol2); atoms read
(34), bonds read (34).`
(HOX) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) ``
(HOX) ``
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) `Info: Total number of electrons: 126; net charge: 0`
(HOX) ``
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) ``
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.4/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) ``
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) ``
Charges for residue HOX determined
Assigning partial charges to residue CRO+LEU+VAL (net charge +0) with am1-bcc
method
CRO+LEU+VAL: number of electrons (315) + formal charge (+0) is odd; cannot
compute charges for radical species using AM1-BCC method
> close session
> open C:/Users/brownekm/Downloads/5bt0.cif
Summary of feedback from opening C:/Users/brownekm/Downloads/5bt0.cif
---
warning | Expected gap or linking atom in CRO /A:66 for LEU /A:64
5bt0.cif title:
Switching GFP fluorescence using genetically encoded phenyl azide chemistry
through two different non-native post-translational modifications routes at
the same position. [more info...]
Chain information for 5bt0.cif #1
---
Chain | Description | UniProt
A B | Green fluorescent protein | A0A059PIQ0_AEQVI
Non-standard residues in 5bt0.cif #1
---
CRO —
{2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (peptide derived chromophore)
SO4 — sulfate ion
5bt0.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 4055 atom radii, 3788 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 5bt0.cif #1
---
warning | Not adding hydrogens to /A GLU 142 CB because it is missing heavy-
atom bond partners
notes | Termini for 5bt0.cif (#1) chain A determined from SEQRES records
Termini for 5bt0.cif (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A SER 2, /B SER 2
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASP 234, /B ASP 234
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A ASP 234
Missing OXT added to C-terminal residue /B ASP 234
445 hydrogen bonds
3594 hydrogens added
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A GLU 142 CD
/A GLU 142 OE2
/A GLU 142 CG
/A GLU 142 OE1
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HOX (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.4/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpo_vvk0s7\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpo_vvk0s7\ante.out.mol2 -fo mol2 -c
bcc -nc 0 -j 5 -s 2 -dr n
(HOX) ``
(HOX) `Welcome to antechamber 20.0: molecular input file processor.`
(HOX) ``
(HOX) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpo_vvk0s7\ante.in.mol2); atoms read
(34), bonds read (34).`
(HOX) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) ``
(HOX) ``
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) `Info: Total number of electrons: 126; net charge: 0`
(HOX) ``
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) ``
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.4/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) ``
(HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HOX) `bash.exe: warning: could not find /tmp, please create!`
(HOX) ``
Charges for residue HOX determined
Assigning partial charges to residue CRO+LEU+VAL (net charge +0) with am1-bcc
method
CRO+LEU+VAL: number of electrons (315) + formal charge (+0) is odd; cannot
compute charges for radical species using AM1-BCC method
> close session
> open C:/Users/brownekm/Downloads/asfd.pdb
Chain information for asfd.pdb #1
---
Chain | Description
B | No description available
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 3303 atom radii, 3393 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 asfd.pdb #1
---
notes | No usable SEQRES records for asfd.pdb (#1) chain B; guessing termini
instead
Chain-initial residues that are actual N termini: /B HIS 28
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: /B ALA 172
345 hydrogen bonds
/B ALA 172 is not terminus, removing H atom from 'C'
3116 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /B ALA 172 H bonded to atom that should not have hydrogens (/B ALA
172 C)
> close session
> open C:/Users/brownekm/Downloads/1ere-gmx.pdb
Summary of feedback from opening C:/Users/brownekm/Downloads/1ere-gmx.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK THIS IS A SIMULATION BOX
1ere-gmx.pdb title:
Giant Rising Ordinary Mutants for A Clerical Setup [more info...]
Chain information for 1ere-gmx.pdb #1
---
Chain | Description
A B | No description available
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 7626 atom radii, 7690 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 1ere-gmx.pdb #1
---
notes | No usable SEQRES records for 1ere-gmx.pdb (#1) chain A; guessing
termini instead
No usable SEQRES records for 1ere-gmx.pdb (#1) chain B; guessing termini
instead
Chain-initial residues that are actual N termini: /A SER 305, /B SER 305
Chain-initial residues that are not actual N termini: /A PHE 337, /A THR 465,
/B PHE 337, /B THR 465
Chain-final residues that are actual C termini: /A ARG 548, /B ARG 548
Chain-final residues that are not actual C termini: /A GLU 330, /A PHE 461, /B
GLU 330, /B PHE 461
437 hydrogen bonds
Adding 'H' to /A PHE 337
Adding 'H' to /A THR 465
Adding 'H' to /B PHE 337
Adding 'H' to /B THR 465
2 hydrogens added
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ILE 326
/A ILE 358
/A ILE 386
/A ILE 389
/A ILE 424
/A ILE 451
/A ILE 452
/A ILE 475
/A ILE 482
/A ILE 487
/A ILE 510
/A ILE 514
/A ARG 548
/B ILE 326
/B ILE 358
/B ILE 386
/B ILE 389
/B ILE 424
/B ILE 451
/B ILE 452
/B ILE 475
/B ILE 482
/B ILE 487
/B ILE 510
/B ILE 514
/B ARG 548
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /B CYS 381 HG1 bonded to atom that should not have hydrogens (/B CYS
381 SG)
> close session
> open "C:/Users/brownekm/Downloads/DysF (pi cat stack).stl .pdb"
Summary of feedback from opening C:/Users/brownekm/Downloads/DysF (pi cat
stack).stl .pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK This pdb file has been created with Blender and the addon Atomic
Blender - PDB
Ignored bad PDB record found on line 2
REMARK For more details see
wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB
> preset nih3d "surface hydrophobicity"
Using preset: NIH3D / Surface Hydrophobicity
Changed 0 atom radii, 0 bond radii, 0 pseudobond radii
Changed 0 pseudobond dashes
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
No atoms specified
Preset expands to these ChimeraX commands:
~struts
~hbonds
size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
style dashes 7
graphics bgcolor white
color name marine 0,50,100
color name forest 13.3,54.5,13.3
color name tangerine 95.3,51.8,0
color name grape 64.3,0,86.7
color name nih_blue 12.5,33.3,54.1
color name jmol_carbon 56.5,56.5,56.5
color name bond_purple 57.6,43.9,85.9
color name struts_grey 48,48,48
color name carbon_grey 22.2,22.2,22.2
surface close
preset 'initial styles' 'original look'
delete solvent
hide H|ligand|~(protein|nucleic-acid) atoms
~nuc
~ribbon
~display
color magenta
color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta
> open "C:\Users\brownekm\Downloads\DysF (pi cat stack).stl .pdb" format pdb
Summary of feedback from opening C:\Users\brownekm\Downloads\DysF (pi cat
stack).stl .pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK This pdb file has been created with Blender and the addon Atomic
Blender - PDB
Ignored bad PDB record found on line 2
REMARK For more details see
wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB
> open "C:/Users/brownekm/Downloads/DysF (pi cat stack).stl .pdb"
Summary of feedback from opening C:/Users/brownekm/Downloads/DysF (pi cat
stack).stl .pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK This pdb file has been created with Blender and the addon Atomic
Blender - PDB
Ignored bad PDB record found on line 2
REMARK For more details see
wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB
> open C:/Users/brownekm/Downloads/DysF.pdb
Summary of feedback from opening C:/Users/brownekm/Downloads/DysF.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK This pdb file has been created with Blender and the addon Atomic
Blender - PDB
Ignored bad PDB record found on line 2
REMARK For more details see
wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB
> open
Missing or invalid "fileNames" argument: Expected a file name
> 4W5Q
Unknown command: 4W5Q
> open 4W5Q
Summary of feedback from opening 4W5Q fetched from pdb
---
notes | Fetching compressed mmCIF 4w5q from
http://files.rcsb.org/download/4w5q.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD IPH from http://ligand-expo.rcsb.org/reports/I/IPH/IPH.cif
4w5q title:
The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA
Containing Seed Pairing from 2-8 [more info...]
Chain information for 4w5q #1
---
Chain | Description | UniProt
A | Protein argonaute-2 | AGO2_HUMAN
B | RNA (5'-R(P*up*up*CP*ap*CP*ap*up*up*GP*CP*CP*CP*ap*ap*GP*up*CP*U)-3') |
D | RNA (5'-R(*ap*ap*ap*up*GP*up*GP*ap*ap*A)-3') |
Non-standard residues in 4w5q #1
---
IPH — phenol
MG — magnesium ion
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 7042 atom radii, 7256 bond radii, 8 pseudobond radii
Changed 2 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 4w5q #1
---
notes | Termini for 4w5q (#1) chain A determined from SEQRES records
Termini for 4w5q (#1) chain B determined from SEQRES records
Termini for 4w5q (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A ALA 22, /A ILE 127,
/A LYS 276, /A VAL 304, /A ASP 838
Chain-final residues that are actual C termini: /A ALA 859
Chain-final residues that are not actual C termini: /A PRO 120, /A ILE 269, /A
LEU 296, /A GLU 821
760 hydrogen bonds
Adding 'H' to /A ALA 22
Adding 'H' to /A ILE 127
Adding 'H' to /A LYS 276
Adding 'H' to /A VAL 304
Adding 'H' to /A ASP 838
6826 hydrogens added
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/D A 10
Deleting 5' phosphates from: /B U 1
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /D A 10 H5' bonded to atom that should not have hydrogens (/D A 10
O5')
> close session
> open 4R8I
Summary of feedback from opening 4R8I fetched from pdb
---
notes | Fetching compressed mmCIF 4r8i from
http://files.rcsb.org/download/4r8i.cif
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif
Fetching CCD SR from http://ligand-expo.rcsb.org/reports/S/SR/SR.cif
Fetching CCD K from http://ligand-expo.rcsb.org/reports/K/K/K.cif
Fetching CCD 0G from http://ligand-expo.rcsb.org/reports/0/0G/0G.cif
Fetching CCD 0C from http://ligand-expo.rcsb.org/reports/0/0C/0C.cif
Fetching CCD 0A from http://ligand-expo.rcsb.org/reports/0/0A/0A.cif
Fetching CCD 0U from http://ligand-expo.rcsb.org/reports/0/0U/0U.cif
Fetching CCD 0U1 from http://ligand-expo.rcsb.org/reports/0/0U1/0U1.cif
4r8i title:
High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in
Complex with the Chemokine CCL2 [more info...]
Chain information for 4r8i #1
---
Chain | Description | UniProt
A | C-C motif chemokine 2 | CCL2_HUMAN
B | Mirror-Image RNA Oligonucleotide Aptamer NOXE36 |
Non-standard residues in 4r8i #1
---
0A — L-adenosine-5'-monophosphate
0U1 — 2'-methylselenyl-2'-deoxy-L-uridine-5'-monophosphate
K — potassium ion
NA — sodium ion
SR — strontium ion
> preset nih3d "surface coulombic"
Using preset: NIH3D / Surface Coulombic
Changed 1515 atom radii, 1506 bond radii, 35 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 4r8i #1
---
warning | Unknown hybridization for atom (SE) of residue type 0U1; not adding
hydrogens to it
notes | Termini for 4r8i (#1) chain A determined from SEQRES records
Termini for 4r8i (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A ASP 3
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A GLN 70
124 hydrogen bonds
Adding 'H' to /A ASP 3
/A GLN 70 is not terminus, removing H atom from 'C'
989 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1200, in <lambda>
run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower()))))
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\preset_mgr\cmd.py", line 50, in preset_cmd
run_preset(session, cat, matches[0])
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\preset_mgr\cmd.py", line 71, in run_preset
session.presets.preset_function(category, preset)()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\preset_mgr\manager.py", line 60, in cb
bi.run_provider(self.session, name, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\nih_presets\\__init__.py", line 22, in run_provider
run_preset(session, name, mgr, **kw)
File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\nih_presets\presets.py", line 302, in run_preset
mgr.execute(cmd)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\preset_mgr\manager.py", line 88, in execute
run(self.session, line, log=False)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 99, in assign_charges
add_charges(session, charged_residues, method=charge_method, status=status,
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 23, in add_charges
uncharged_res_types = add_standard_charges(session, residues, status=status,
query_user=query_user,
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 198, in add_standard_charges
fr = FakeRes(connected)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 775, in __init__
raise ValueError("Could not come up with unique atom name in mega-residue")
ValueError: Could not come up with unique atom name in mega-residue
ValueError: Could not come up with unique atom name in mega-residue
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 775, in __init__
raise ValueError("Could not come up with unique atom name in mega-residue")
See log for complete Python traceback.
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 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
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
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-NIHPresets: 1.1.5
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
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
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (3)
follow-up: 1 comment:1 by , 3 years ago
comment:2 by , 3 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Could not come up with unique atom name in mega-residue |
comment:3 by , 3 years ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
The entire 40-residue nucleic acid moiety in 4r8i is composed of non-standard residues that would have to be assigned charges as a unit. The current algorithm can't come up with reasonable unique atom names across the combined mega-residue, which is probably a good thing since you would never want to send a monster like that to AM1-BCC, and possibly not Gasteiger. It now throws ChargeError in this case instead of ValueError, so NIH3D will skip it.
Did some monkeying around to see if Gasteiger could handle it if unique atom names were assigned, and this moiety exceeded various builtin limits for Gasteiger, so its uncertain how accurate the charges are, but it did finish and produce seemingly reasonable charges. However, I had to change a selenium to sulfur first, since neither charge model can handle selenium -- so NIH3D will be skipping this one regardless.
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Note -> I did try this in the daily build from 11/22/2022 as well, but when I tried to submit an error report the software crashed, so I just submitted the same thing from the LTS instead. -----Original Message----- From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: Wednesday, November 23, 2022 9:51 AM To: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov> Subject: [EXTERNAL] [ChimeraX] #8073: ChimeraX bug report submission #8073: ChimeraX bug report submission ------------------------------+----------------------------- Reporter: kristen.browne@... | Type: defect Status: new | Priority: normal Component: Unassigned | Blocked By: Blocking: | Notify when closed: ------------------------------+----------------------------- {{{ The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description open 4R8I Had a similar error before with mol2 file that was fixed in ticket: https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8022&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=n6BtLNaF9x5nleh0nJSO1OjmCFkAvF%2BWbmCBaSAzeF8%3D&reserved=0 Might not be fixable and need to just skip Coulombic, but thought I'd check. Log: UCSF ChimeraX version: 1.4 (2022-06-03) (c) 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3OE0 Summary of feedback from opening 3OE0 fetched from pdb --- notes | Fetching compressed mmCIF 3oe0 from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffiles.rcsb.org%2Fdownload%2F3oe0.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=J5LWpImKNx%2FyuPkO06Ewio%2FcgSQ433Z8PesIhwkMkhE%3D&reserved=0 Fetching CCD ALN from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FA%2FALN%2FALN.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZP7o%2FDoZmdsRbuGbyVRrmeLsNbnPieqN58CyQffI2eU%3D&reserved=0 Fetching CCD DPR from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FD%2FDPR%2FDPR.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ciDC0zRVgMpI8ydc%2BR%2BQX0WzeOUR0v6Zz4cEPV4P4PQ%3D&reserved=0 Fetching CCD CIR from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FC%2FCIR%2FCIR.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hrUkUI2IwXNvz7dYNoqO2roWbk92PJcWhbOHxI7QQTI%3D&reserved=0 3oe0 title: Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide antagonist CVX15 [more info...] Chain information for 3oe0 #1 --- Chain | Description | UniProt A | C-X-C chemokine receptor type 4, Lysozyme Chimera | CXCR4_HUMAN I | Polyphemusin analog, CXC chemokine receptor antagonist | 3oe0 mmCIF Assemblies --- 1| author_defined_assembly > preset nih3d "surface coulombic" Using preset: NIH3D / Surface Coulombic Changed 3640 atom radii, 3728 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 3oe0 #1 --- warnings | Not adding hydrogens to /A GLN 233 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A LYS 234 CB because it is missing heavy-atom bond partners notes | Termini for 3oe0 (#1) chain A determined from SEQRES records Termini for 3oe0 (#1) chain I determined from SEQRES records Chain-initial residues that are actual N termini: /I ARG 1 Chain-initial residues that are not actual N termini: /A LYS 25, /A SER 71, /A GLY 231 Chain-final residues that are actual C termini: /I DPR 16 Chain-final residues that are not actual C termini: /A GLN 66, /A TYR 1161, /A ALA 303 436 hydrogen bonds Adding 'H' to /A LYS 25 Adding 'H' to /A SER 71 Adding 'H' to /A GLY 231 /A ALA 303 is not terminus, removing H atom from 'C' 3686 hydrogens added The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A LYS 234 CD /A LYS 234 CE /A LYS 234 CG /A LYS 234 NZ /A GLN 233 CD /A GLN 233 CG /A GLN 233 OE1 /A GLN 233 NE2 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue ALN (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.4/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\brownekm\AppData\Local\Temp\1\tmp__qs84dv\ante.in.mol2 -fi mol2 -o C:\Users\brownekm\AppData\Local\Temp\1\tmp__qs84dv\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (ALN) `` (ALN) `Welcome to antechamber 20.0: molecular input file processor.` (ALN) `` (ALN) `Info: Finished reading file (C:\Users\brownekm\AppData\Local\Temp\1\tmp__qs84dv\ante.in.mol2); atoms read (38), bonds read (39).` (ALN) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (ALN) `bash.exe: warning: could not find /tmp, please create!` (ALN) `` (ALN) `` (ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (ALN) `bash.exe: warning: could not find /tmp, please create!` (ALN) `Info: Total number of electrons: 144; net charge: 0` (ALN) `` (ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out` (ALN) `bash.exe: warning: could not find /tmp, please create!` (ALN) `` (ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX 1.4/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1` (ALN) `bash.exe: warning: could not find /tmp, please create!` (ALN) `` (ALN) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (ALN) `bash.exe: warning: could not find /tmp, please create!` (ALN) `` Charges for residue ALN determined Assigning partial charges to residue CIR+ARG+CYS (net charge +2) with am1-bcc method CIR+ARG+CYS: number of electrons (287) + formal charge (+2) is odd; cannot compute charges for radical species using AM1-BCC method > close session > open 5BT0 Summary of feedback from opening 5BT0 fetched from pdb --- notes | Fetching compressed mmCIF 5bt0 from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffiles.rcsb.org%2Fdownload%2F5bt0.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TRpnJO%2F54ot6f0RO4N3tz9IFKXWd9a9T2DlDsKelBQ0%3D&reserved=0 Fetching CCD CRO from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FC%2FCRO%2FCRO.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=r8cEqKpnY7RRmTODfcdaYwyqOCdScIiUnfBPs5P9EBA%3D&reserved=0 Fetching CCD HOX from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FH%2FHOX%2FHOX.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2MrQndYQtAUozUXOr2Ldu%2Byib%2BRBWpNXdAYVgjMe3HE%3D&reserved=0 5bt0 title: Switching GFP fluorescence using genetically encoded phenyl azide chemistry through two different non-native post-translational modifications routes at the same position. [more info...] Chain information for 5bt0 #1 --- Chain | Description | UniProt A B | Green fluorescent protein | A0A059PIQ0_AEQVI Non-standard residues in 5bt0 #1 --- CRO - {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5 -dihydro-1H-imidazol-1-yl}acetic acid (peptide derived chromophore) SO4 - sulfate ion 5bt0 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > preset nih3d "surface coulombic" Using preset: NIH3D / Surface Coulombic Changed 4055 atom radii, 3788 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 5bt0 #1 --- warning | Not adding hydrogens to /A GLU 142 CB because it is missing heavy- atom bond partners notes | Termini for 5bt0 (#1) chain A determined from SEQRES records Termini for 5bt0 (#1) chain B determined from SEQRES records Chain-initial residues that are actual N termini: /A SER 2, /B SER 2 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASP 234, /B ASP 234 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A ASP 234 Missing OXT added to C-terminal residue /B ASP 234 445 hydrogen bonds 3594 hydrogens added The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A GLU 142 CD /A GLU 142 OE2 /A GLU 142 CG /A GLU 142 OE1 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HOX (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.4/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\brownekm\AppData\Local\Temp\1\tmp4jrgi1ju\ante.in.mol2 -fi mol2 -o C:\Users\brownekm\AppData\Local\Temp\1\tmp4jrgi1ju\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HOX) `` (HOX) `Welcome to antechamber 20.0: molecular input file processor.` (HOX) `` (HOX) `Info: Finished reading file (C:\Users\brownekm\AppData\Local\Temp\1\tmp4jrgi1ju\ante.in.mol2); atoms read (34), bonds read (34).` (HOX) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `` (HOX) `` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `Info: Total number of electrons: 126; net charge: 0` (HOX) `` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX 1.4/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `` Charges for residue HOX determined Assigning partial charges to residue CRO+LEU+VAL (net charge +0) with am1-bcc method CRO+LEU+VAL: number of electrons (315) + formal charge (+0) is odd; cannot compute charges for radical species using AM1-BCC method > close session > open C:/Users/brownekm/Downloads/5bt0.cif Summary of feedback from opening C:/Users/brownekm/Downloads/5bt0.cif --- warning | Expected gap or linking atom in CRO /A:66 for LEU /A:64 5bt0.cif title: Switching GFP fluorescence using genetically encoded phenyl azide chemistry through two different non-native post-translational modifications routes at the same position. [more info...] Chain information for 5bt0.cif #1 --- Chain | Description | UniProt A B | Green fluorescent protein | A0A059PIQ0_AEQVI Non-standard residues in 5bt0.cif #1 --- CRO - {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5 -dihydro-1H-imidazol-1-yl}acetic acid (peptide derived chromophore) SO4 - sulfate ion 5bt0.cif mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > preset nih3d "surface coulombic" Using preset: NIH3D / Surface Coulombic Changed 4055 atom radii, 3788 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 5bt0.cif #1 --- warning | Not adding hydrogens to /A GLU 142 CB because it is missing heavy- atom bond partners notes | Termini for 5bt0.cif (#1) chain A determined from SEQRES records Termini for 5bt0.cif (#1) chain B determined from SEQRES records Chain-initial residues that are actual N termini: /A SER 2, /B SER 2 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASP 234, /B ASP 234 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A ASP 234 Missing OXT added to C-terminal residue /B ASP 234 445 hydrogen bonds 3594 hydrogens added The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A GLU 142 CD /A GLU 142 OE2 /A GLU 142 CG /A GLU 142 OE1 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HOX (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.4/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\brownekm\AppData\Local\Temp\1\tmpo_vvk0s7\ante.in.mol2 -fi mol2 -o C:\Users\brownekm\AppData\Local\Temp\1\tmpo_vvk0s7\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HOX) `` (HOX) `Welcome to antechamber 20.0: molecular input file processor.` (HOX) `` (HOX) `Info: Finished reading file (C:\Users\brownekm\AppData\Local\Temp\1\tmpo_vvk0s7\ante.in.mol2); atoms read (34), bonds read (34).` (HOX) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `` (HOX) `` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `Info: Total number of electrons: 126; net charge: 0` (HOX) `` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX 1.4/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `` (HOX) `Running: "C:/Program Files/ChimeraX 1.4/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (HOX) `bash.exe: warning: could not find /tmp, please create!` (HOX) `` Charges for residue HOX determined Assigning partial charges to residue CRO+LEU+VAL (net charge +0) with am1-bcc method CRO+LEU+VAL: number of electrons (315) + formal charge (+0) is odd; cannot compute charges for radical species using AM1-BCC method > close session > open C:/Users/brownekm/Downloads/asfd.pdb Chain information for asfd.pdb #1 --- Chain | Description B | No description available > preset nih3d "surface coulombic" Using preset: NIH3D / Surface Coulombic Changed 3303 atom radii, 3393 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 asfd.pdb #1 --- notes | No usable SEQRES records for asfd.pdb (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /B HIS 28 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: /B ALA 172 345 hydrogen bonds /B ALA 172 is not terminus, removing H atom from 'C' 3116 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /B ALA 172 H bonded to atom that should not have hydrogens (/B ALA 172 C) > close session > open C:/Users/brownekm/Downloads/1ere-gmx.pdb Summary of feedback from opening C:/Users/brownekm/Downloads/1ere-gmx.pdb --- warning | Ignored bad PDB record found on line 2 REMARK THIS IS A SIMULATION BOX 1ere-gmx.pdb title: Giant Rising Ordinary Mutants for A Clerical Setup [more info...] Chain information for 1ere-gmx.pdb #1 --- Chain | Description A B | No description available > preset nih3d "surface coulombic" Using preset: NIH3D / Surface Coulombic Changed 7626 atom radii, 7690 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 1ere-gmx.pdb #1 --- notes | No usable SEQRES records for 1ere-gmx.pdb (#1) chain A; guessing termini instead No usable SEQRES records for 1ere-gmx.pdb (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A SER 305, /B SER 305 Chain-initial residues that are not actual N termini: /A PHE 337, /A THR 465, /B PHE 337, /B THR 465 Chain-final residues that are actual C termini: /A ARG 548, /B ARG 548 Chain-final residues that are not actual C termini: /A GLU 330, /A PHE 461, /B GLU 330, /B PHE 461 437 hydrogen bonds Adding 'H' to /A PHE 337 Adding 'H' to /A THR 465 Adding 'H' to /B PHE 337 Adding 'H' to /B THR 465 2 hydrogens added The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A ILE 326 /A ILE 358 /A ILE 386 /A ILE 389 /A ILE 424 /A ILE 451 /A ILE 452 /A ILE 475 /A ILE 482 /A ILE 487 /A ILE 510 /A ILE 514 /A ARG 548 /B ILE 326 /B ILE 358 /B ILE 386 /B ILE 389 /B ILE 424 /B ILE 451 /B ILE 452 /B ILE 475 /B ILE 482 /B ILE 487 /B ILE 510 /B ILE 514 /B ARG 548 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /B CYS 381 HG1 bonded to atom that should not have hydrogens (/B CYS 381 SG) > close session > open "C:/Users/brownekm/Downloads/DysF (pi cat stack).stl .pdb" Summary of feedback from opening C:/Users/brownekm/Downloads/DysF (pi cat stack).stl .pdb --- warnings | Ignored bad PDB record found on line 1 REMARK This pdb file has been created with Blender and the addon Atomic Blender - PDB Ignored bad PDB record found on line 2 REMARK For more details see wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB > preset nih3d "surface hydrophobicity" Using preset: NIH3D / Surface Hydrophobicity Changed 0 atom radii, 0 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. No atoms specified Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent hide H|ligand|~(protein|nucleic-acid) atoms ~nuc ~ribbon ~display color magenta color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta > open "C:\Users\brownekm\Downloads\DysF (pi cat stack).stl .pdb" format pdb Summary of feedback from opening C:\Users\brownekm\Downloads\DysF (pi cat stack).stl .pdb --- warnings | Ignored bad PDB record found on line 1 REMARK This pdb file has been created with Blender and the addon Atomic Blender - PDB Ignored bad PDB record found on line 2 REMARK For more details see wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB > open "C:/Users/brownekm/Downloads/DysF (pi cat stack).stl .pdb" Summary of feedback from opening C:/Users/brownekm/Downloads/DysF (pi cat stack).stl .pdb --- warnings | Ignored bad PDB record found on line 1 REMARK This pdb file has been created with Blender and the addon Atomic Blender - PDB Ignored bad PDB record found on line 2 REMARK For more details see wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB > open C:/Users/brownekm/Downloads/DysF.pdb Summary of feedback from opening C:/Users/brownekm/Downloads/DysF.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK This pdb file has been created with Blender and the addon Atomic Blender - PDB Ignored bad PDB record found on line 2 REMARK For more details see wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB > open Missing or invalid "fileNames" argument: Expected a file name > 4W5Q Unknown command: 4W5Q > open 4W5Q Summary of feedback from opening 4W5Q fetched from pdb --- notes | Fetching compressed mmCIF 4w5q from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffiles.rcsb.org%2Fdownload%2F4w5q.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mUgOjSXH8lnF056cN9mIh5CZESVQFhhM9KPhDW9%2FPWs%3D&reserved=0 Fetching CCD MG from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FM%2FMG%2FMG.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QOqiuyu5ZiseJnygGp9ws9aEV%2FaSqddifJw%2F3m7rhac%3D&reserved=0 Fetching CCD IPH from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FI%2FIPH%2FIPH.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TuuBhEggVUY%2FdmtiBVd9L351GbkgnrPM3qSmDvH2mQY%3D&reserved=0 4w5q title: The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed Pairing from 2-8 [more info...] Chain information for 4w5q #1 --- Chain | Description | UniProt A | Protein argonaute-2 | AGO2_HUMAN B | RNA (5'-R(P*up*up*CP*ap*CP*ap*up*up*GP*CP*CP*CP*ap*ap*GP*up*CP*U)-3') | D | RNA (5'-R(*ap*ap*ap*up*GP*up*GP*ap*ap*A)-3') | Non-standard residues in 4w5q #1 --- IPH - phenol MG - magnesium ion > preset nih3d "surface coulombic" Using preset: NIH3D / Surface Coulombic Changed 7042 atom radii, 7256 bond radii, 8 pseudobond radii Changed 2 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 4w5q #1 --- notes | Termini for 4w5q (#1) chain A determined from SEQRES records Termini for 4w5q (#1) chain B determined from SEQRES records Termini for 4w5q (#1) chain D determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A ALA 22, /A ILE 127, /A LYS 276, /A VAL 304, /A ASP 838 Chain-final residues that are actual C termini: /A ALA 859 Chain-final residues that are not actual C termini: /A PRO 120, /A ILE 269, /A LEU 296, /A GLU 821 760 hydrogen bonds Adding 'H' to /A ALA 22 Adding 'H' to /A ILE 127 Adding 'H' to /A LYS 276 Adding 'H' to /A VAL 304 Adding 'H' to /A ASP 838 6826 hydrogens added The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /D A 10 Deleting 5' phosphates from: /B U 1 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /D A 10 H5' bonded to atom that should not have hydrogens (/D A 10 O5') > close session > open 4R8I Summary of feedback from opening 4R8I fetched from pdb --- notes | Fetching compressed mmCIF 4r8i from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffiles.rcsb.org%2Fdownload%2F4r8i.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RLPh35DkcB7E7g8k29OuM9oC9ElnzIPWwao4I9OHJVs%3D&reserved=0 Fetching CCD NA from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FN%2FNA%2FNA.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WyfdHuAZzY%2BdLeFU2S6EuPT3s%2FyukQOK16QjMJDdwqU%3D&reserved=0 Fetching CCD SR from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FS%2FSR%2FSR.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=DDYmdFfLHT3UPaiZPYHddJDY9ceL2vYofE6s%2BfCp7eE%3D&reserved=0 Fetching CCD K from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2FK%2FK%2FK.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637465635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=985kSzpCa4G2wbzDuxaPa3XP0FVQPk51DwLDqgNapLY%3D&reserved=0 Fetching CCD 0G from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2F0%2F0G%2F0G.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637622739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XejrtxCsyd2PHhgHs70lHGISLSqhcVYiH3E3vVTSq9s%3D&reserved=0 Fetching CCD 0C from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2F0%2F0C%2F0C.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637622739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FxDc6QYbDEOfJKBTQFyFwbUcseD3wx3BafsblU%2FORrQ%3D&reserved=0 Fetching CCD 0A from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2F0%2F0A%2F0A.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637622739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZrH%2BAnMYegeDFCISdSRpoKEp13Xc1ekrLGXQiqaUICY%3D&reserved=0 Fetching CCD 0U from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2F0%2F0U%2F0U.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637622739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EWNyssghYmbr8%2FQ3XuKW2QZ9tukTlyknCt4DeuQWHB0%3D&reserved=0 Fetching CCD 0U1 from https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fligand-expo.rcsb.org%2Freports%2F0%2F0U1%2F0U1.cif&data=05%7C01%7Ckristen.browne%40nih.gov%7C0e932c1ae94a41be9a7208dacd6222e9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638048118637622739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UjvFscdRCiLVmYUwuatB9ffhdMuH73o4f%2FFQUXRF69c%3D&reserved=0 4r8i title: High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2 [more info...] Chain information for 4r8i #1 --- Chain | Description | UniProt A | C-C motif chemokine 2 | CCL2_HUMAN B | Mirror-Image RNA Oligonucleotide Aptamer NOXE36 | Non-standard residues in 4r8i #1 --- 0A - L-adenosine-5'-monophosphate 0U1 - 2'-methylselenyl-2'-deoxy-L-uridine-5'-monophosphate K - potassium ion NA - sodium ion SR - strontium ion > preset nih3d "surface coulombic" Using preset: NIH3D / Surface Coulombic Changed 1515 atom radii, 1506 bond radii, 35 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 4r8i #1 --- warning | Unknown hybridization for atom (SE) of residue type 0U1; not adding hydrogens to it notes | Termini for 4r8i (#1) chain A determined from SEQRES records Termini for 4r8i (#1) chain B determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A ASP 3 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLN 70 124 hydrogen bonds Adding 'H' to /A ASP 3 /A GLN 70 is not terminus, removing H atom from 'C' 989 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\gui.py", line 1200, in <lambda> run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower())))) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\preset_mgr\cmd.py", line 50, in preset_cmd run_preset(session, cat, matches[0]) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\preset_mgr\cmd.py", line 71, in run_preset session.presets.preset_function(category, preset)() File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\preset_mgr\manager.py", line 60, in cb bi.run_provider(self.session, name, self) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\toolshed\info.py", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.4\site- packages\chimerax\nih_presets\\__init__.py", line 22, in run_provider run_preset(session, name, mgr, **kw) File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.4\site- packages\chimerax\nih_presets\presets.py", line 302, in run_preset mgr.execute(cmd) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\preset_mgr\manager.py", line 88, in execute run(self.session, line, log=False) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\coulombic\coulombic.py", line 99, in assign_charges add_charges(session, charged_residues, method=charge_method, status=status, File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\add_charge\charge.py", line 23, in add_charges uncharged_res_types = add_standard_charges(session, residues, status=status, query_user=query_user, File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\add_charge\charge.py", line 198, in add_standard_charges fr = FakeRes(connected) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\add_charge\charge.py", line 775, in __init__ raise ValueError("Could not come up with unique atom name in mega- residue") ValueError: Could not come up with unique atom name in mega-residue ValueError: Could not come up with unique atom name in mega-residue File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\add_charge\charge.py", line 775, in __init__ raise ValueError("Could not come up with unique atom name in mega- residue") See log for complete Python traceback. 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 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 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 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2022.5.18.1 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-NIHPresets: 1.1.5 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pywin32: 303 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 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