id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8073 Could not come up with unique atom name in mega-residue kristen.browne@… Eric Pettersen "{{{ 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 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 }}} " defect closed normal Structure Editing limitation all ChimeraX