Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8026 closed defect (fixed)

sqm failure on all-nonstandard nucleic acid

Reported by: kristen.browne@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202210260016 (2022-10-26 00:16:05 UTC)
Description
Failure running coulombic preset on pdb 6GN4.
Chimera was ok according to 3DPX:
https://3dprint.nih.gov/discover/3DPX-009585


Log:
UCSF ChimeraX version: 1.6.dev202210260016 (2022-10-26)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6GN4 format mmcif fromDatabase pdb

6gn4 title:  
tc-DNA/tc-DNA duplex [more info...]  
  
Chain information for 6gn4  
---  
Chain | Description  
1.1/A | Tc-DNA
(5'-D(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3')  
1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Tc-DNA
(5'-D(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3')  
1.1/B | Tc-DNA
(5'-D(*(TCS)P*(TTK)P*(TCY)P*(TCY)P*(TCS)P*(TCJ)P*(TCJ)P*(TCS)P*(TCY)P*(TCS))-3')  
1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B | Tc-DNA
(5'-D(*(TCS)P*(TTK)P*(TCY)P*(TCY)P*(TCS)P*(TCJ)P*(TCJ)P*(TCS)P*(TCY)P*(TCS))-3')  
  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 7500 atom radii, 8380 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  
Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  
Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400

  
Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd

  
Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a

  
Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090

  
Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db

  
Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a

  
Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Nothing selected  
[Repeated 1 time(s)]Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    delete H
    preset 'initial styles' cartoon
    nucleotides ladder radius 1.2
    color white target abc
    color helix marine
    color strand firebrick
    color coil goldenrod
    color nucleic-acid forest
    color :A:C:G:U grape
    color byatom
    select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide)
    color sel carbon_grey atoms
    color ligand | protein & sideonly byhet atoms
    ~select
    rainbow #1.1@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.2@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.3@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.4@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.5@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.6@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.7@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.8@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.9@ca,c4' chains palette marine:goldenrod target rs
    rainbow #1.10@ca,c4' chains palette marine:goldenrod target rs

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 4700 atom radii, 5580 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 6gn4 #1.1  
---  
notes | Termini for 6gn4 (#1.1) chain A determined from SEQRES records  
Termini for 6gn4 (#1.1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.2  
---  
notes | Termini for 6gn4 (#1.2) chain A determined from SEQRES records  
Termini for 6gn4 (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.3  
---  
notes | Termini for 6gn4 (#1.3) chain A determined from SEQRES records  
Termini for 6gn4 (#1.3) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.4  
---  
notes | Termini for 6gn4 (#1.4) chain A determined from SEQRES records  
Termini for 6gn4 (#1.4) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.5  
---  
notes | Termini for 6gn4 (#1.5) chain A determined from SEQRES records  
Termini for 6gn4 (#1.5) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.6  
---  
notes | Termini for 6gn4 (#1.6) chain A determined from SEQRES records  
Termini for 6gn4 (#1.6) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.7  
---  
notes | Termini for 6gn4 (#1.7) chain A determined from SEQRES records  
Termini for 6gn4 (#1.7) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.8  
---  
notes | Termini for 6gn4 (#1.8) chain A determined from SEQRES records  
Termini for 6gn4 (#1.8) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.9  
---  
notes | Termini for 6gn4 (#1.9) chain A determined from SEQRES records  
Termini for 6gn4 (#1.9) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
280 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.10  
---  
notes | Termini for 6gn4 (#1.10) chain A determined from SEQRES records  
Termini for 6gn4 (#1.10) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
280 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ
(net charge -9) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpvn348hf2\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpvn348hf2\ante.out.mol2 -fo mol2 -c
bcc -nc -9 -j 5 -s 2 -dr n  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Welcome to antechamber 20.0:
molecular input file processor.`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpvn348hf2\ante.in.mol2); atoms read
(375), bonds read (417).`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Info: Determining atomic numbers
from atomic symbols which are case sensitive.`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Running: "C:/Program
Files/ChimeraX/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0
-o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `bash.exe: warning: could not find
/tmp, please create!`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Running: "C:/Program
Files/ChimeraX/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `bash.exe: warning: could not find
/tmp, please create!`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Info: Total number of electrons:
1778; net charge: -9`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Running: "C:/Program
Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `bash.exe: warning: could not find
/tmp, please create!`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `/usr/bin/antechamber: Fatal Error!`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Unable to find sqm charges in file
(sqm.out).`  
(EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Verify the filename and the file
contents.`  
Failure running ANTECHAMBER for residue
EAN+F7H+TCJ+F4Q+F4Q+TCJ+EAN+EAN+TCY+TCJ  
Check reply log for details  

> close session

> open 6GN4

6gn4 title:  
tc-DNA/tc-DNA duplex [more info...]  
  
Chain information for 6gn4  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Tc-DNA
(5'-D(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3')  
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B | Tc-DNA
(5'-D(*(TCS)P*(TTK)P*(TCY)P*(TCY)P*(TCS)P*(TCJ)P*(TCJ)P*(TCS)P*(TCY)P*(TCS))-3')  
  

> preset nih3d "surface by chain"

Using preset: NIH3D / Surface by Chain  
Changed 7500 atom radii, 8380 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 6gn4 #1.1  
---  
notes | Termini for 6gn4 (#1.1) chain A determined from SEQRES records  
Termini for 6gn4 (#1.1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.2  
---  
notes | Termini for 6gn4 (#1.2) chain A determined from SEQRES records  
Termini for 6gn4 (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.3  
---  
notes | Termini for 6gn4 (#1.3) chain A determined from SEQRES records  
Termini for 6gn4 (#1.3) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.4  
---  
notes | Termini for 6gn4 (#1.4) chain A determined from SEQRES records  
Termini for 6gn4 (#1.4) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.5  
---  
notes | Termini for 6gn4 (#1.5) chain A determined from SEQRES records  
Termini for 6gn4 (#1.5) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.6  
---  
notes | Termini for 6gn4 (#1.6) chain A determined from SEQRES records  
Termini for 6gn4 (#1.6) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.7  
---  
notes | Termini for 6gn4 (#1.7) chain A determined from SEQRES records  
Termini for 6gn4 (#1.7) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.8  
---  
notes | Termini for 6gn4 (#1.8) chain A determined from SEQRES records  
Termini for 6gn4 (#1.8) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.9  
---  
notes | Termini for 6gn4 (#1.9) chain A determined from SEQRES records  
Termini for 6gn4 (#1.9) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.10  
---  
notes | Termini for 6gn4 (#1.10) chain A determined from SEQRES records  
Termini for 6gn4 (#1.10) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    addh #1.2
    addh #1.3
    addh #1.4
    addh #1.5
    addh #1.6
    addh #1.7
    addh #1.8
    addh #1.9
    addh #1.10
    surface #1.1 enclose #1.1 grid 0.5 sharp true
    surface #1.2 enclose #1.2 grid 0.5 sharp true
    surface #1.3 enclose #1.3 grid 0.5 sharp true
    surface #1.4 enclose #1.4 grid 0.5 sharp true
    surface #1.5 enclose #1.5 grid 0.5 sharp true
    surface #1.6 enclose #1.6 grid 0.5 sharp true
    surface #1.7 enclose #1.7 grid 0.5 sharp true
    surface #1.8 enclose #1.8 grid 0.5 sharp true
    surface #1.9 enclose #1.9 grid 0.5 sharp true
    surface #1.10 enclose #1.10 grid 0.5 sharp true
    rainbow #1.1@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.1 near #1.1 distance 20
    rainbow #1.2@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.2 near #1.2 distance 20
    rainbow #1.3@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.3 near #1.3 distance 20
    rainbow #1.4@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.4 near #1.4 distance 20
    rainbow #1.5@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.5 near #1.5 distance 20
    rainbow #1.6@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.6 near #1.6 distance 20
    rainbow #1.7@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.7 near #1.7 distance 20
    rainbow #1.8@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.8 near #1.8 distance 20
    rainbow #1.9@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.9 near #1.9 distance 20
    rainbow #1.10@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1.10 near #1.10 distance 20

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 7500 atom radii, 8380 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 6gn4 #1.1  
---  
notes | Termini for 6gn4 (#1.1) chain A determined from SEQRES records  
Termini for 6gn4 (#1.1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.2  
---  
notes | Termini for 6gn4 (#1.2) chain A determined from SEQRES records  
Termini for 6gn4 (#1.2) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.3  
---  
notes | Termini for 6gn4 (#1.3) chain A determined from SEQRES records  
Termini for 6gn4 (#1.3) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.4  
---  
notes | Termini for 6gn4 (#1.4) chain A determined from SEQRES records  
Termini for 6gn4 (#1.4) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.5  
---  
notes | Termini for 6gn4 (#1.5) chain A determined from SEQRES records  
Termini for 6gn4 (#1.5) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.6  
---  
notes | Termini for 6gn4 (#1.6) chain A determined from SEQRES records  
Termini for 6gn4 (#1.6) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.7  
---  
notes | Termini for 6gn4 (#1.7) chain A determined from SEQRES records  
Termini for 6gn4 (#1.7) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
31 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.8  
---  
notes | Termini for 6gn4 (#1.8) chain A determined from SEQRES records  
Termini for 6gn4 (#1.8) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.9  
---  
notes | Termini for 6gn4 (#1.9) chain A determined from SEQRES records  
Termini for 6gn4 (#1.9) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
32 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to 6gn4 #1.10  
---  
notes | Termini for 6gn4 (#1.10) chain A determined from SEQRES records  
Termini for 6gn4 (#1.10) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
30 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ
(net charge -9) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpcdrbtaa3\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpcdrbtaa3\ante.out.mol2 -fo mol2 -c
bcc -nc -9 -j 5 -s 2 -dr n  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Welcome to antechamber 20.0:
molecular input file processor.`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpcdrbtaa3\ante.in.mol2); atoms read
(375), bonds read (417).`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Info: Determining atomic numbers
from atomic symbols which are case sensitive.`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Running: "C:/Program
Files/ChimeraX/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0
-o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `bash.exe: warning: could not find
/tmp, please create!`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Running: "C:/Program
Files/ChimeraX/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `bash.exe: warning: could not find
/tmp, please create!`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Info: Total number of electrons:
1778; net charge: -9`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) ``  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Running: "C:/Program
Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `bash.exe: warning: could not find
/tmp, please create!`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `/usr/bin/antechamber: Fatal Error!`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Unable to find sqm charges in file
(sqm.out).`  
(TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ) `Verify the filename and the file
contents.`  
Failure running ANTECHAMBER for residue
TCJ+EAN+F4Q+F7H+F4Q+TCJ+EAN+EAN+TCY+TCJ  
Check reply log for details  




OpenGL version: 3.3.0 NVIDIA 466.47
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 137,220,087,808
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.43.2
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202210260016
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.25
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.5
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.10.0

Change History (3)

comment:1 by pett, 3 years ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → sqm failure on all-nonstandard nucleic acid

comment:2 by pett, 3 years ago

Resolution: → fixed
Status: accepted → closed

Switched the coulombic preset to use Gasteiger charge-determination method. Sending updated bundle to Michal separately.

Last edited 3 years ago by pett (previous) (diff)

comment:3 by pett, 3 years ago

Um. Michal. (insert red face here)

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