Opened 3 years ago

Closed 3 years ago

#8029 closed defect (fixed)

non-standard C-terminal oxygen name

Reported by: kristen.browne@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc: phil.cruz@…, michal.stolarczyk@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202210260016 (2022-10-26 00:16:05 UTC)
Description
Another non-standard heavy atom name.  This was also reported in issue #8021 so you may want to merge them.  Since they may be different non-standard names, wanted to share this one as well.

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 C:\Users\brownekm\Downloads\6cv7-3.pdb format pdb

Summary of feedback from opening C:\Users\brownekm\Downloads\6cv7-3.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2938 messages similar to the above omitted  
  
Chain information for 6cv7-3.pdb #1  
---  
Chain | Description  
A | No description available  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 5810 atom radii, 5934 bond radii, 6 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 6cv7-3.pdb #1  
---  
notes | No usable SEQRES records for 6cv7-3.pdb (#1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: /A TYR 2  
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: /A ASP 366  
604 hydrogen bonds  
/A ASP 366 is not terminus, removing H atom from 'C'  
5685 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen /A ASP 366 H bonded to atom that should not have hydrogens (/A ASP
366 C)  

> open 5O6U

Summary of feedback from opening 5O6U fetched from pdb  
---  
note | Fetching compressed mmCIF 5o6u from
http://files.rcsb.org/download/5o6u.cif  
  
5o6u title:  
Structure of the Cascade-I-Fv R-loop complex from Shewanella putrefaciens
[more info...]  
  
Chain information for 5o6u #2  
---  
Chain | Description | UniProt  
A | crRNA |  
B | CRISPR-associated protein, Csy4 family | A4Y6G3_SHEPC  
C D E | Uncharacterized protein | A4Y6G1_SHEPC  
F | Uncharacterized protein | A4Y6G2_SHEPC  
H | non-target DNA |  
I | target DNA |  
  

> close session

> open 5O6U format mmcif fromDatabase pdb

5o6u title:  
Structure of the Cascade-I-Fv R-loop complex from Shewanella putrefaciens
[more info...]  
  
Chain information for 5o6u #1  
---  
Chain | Description | UniProt  
A | crRNA |  
B | CRISPR-associated protein, Csy4 family | A4Y6G3_SHEPC  
C D E | Uncharacterized protein | A4Y6G1_SHEPC  
F | Uncharacterized protein | A4Y6G2_SHEPC  
H | non-target DNA |  
I | target DNA |  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 13131 atom radii, 13563 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 5o6u #1  
---  
warnings | Not adding hydrogens to /H DC 2 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /I DG 1 P because it is missing heavy-atom bond
partners  
notes | Termini for 5o6u (#1) chain A determined from SEQRES records  
Termini for 5o6u (#1) chain B determined from SEQRES records  
Termini for 5o6u (#1) chain C determined from SEQRES records  
Termini for 5o6u (#1) chain D determined from SEQRES records  
Termini for 5o6u (#1) chain E determined from SEQRES records  
3 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /B ASN 2, /C MET 1, /D MET
1, /E MET 1, /F MET 1  
Chain-initial residues that are not actual N termini: /C ASP 39, /C LYS 66, /C
LEU 105, /C LYS 163  
Chain-final residues that are actual C termini: /B PHE 183, /C LYS 315, /D LYS
315, /E LYS 315, /F LEU 336  
Chain-final residues that are not actual C termini: /C THR 29, /C GLY 54, /C
GLU 92, /C PHE 146  
Missing OXT added to C-terminal residue /C LYS 315  
Missing OXT added to C-terminal residue /D LYS 315  
Missing OXT added to C-terminal residue /E LYS 315  
Missing OXT added to C-terminal residue /F LEU 336  
1377 hydrogen bonds  
Adding 'H' to /C ASP 39  
Adding 'H' to /C LYS 66  
Adding 'H' to /C LEU 105  
Adding 'H' to /C LYS 163  
12218 hydrogens added  
  

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A C 43  

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen /A C 43 H5' bonded to atom that should not have hydrogens (/A C 43
O5')  

> close session

> open C:/Users/brownekm/Downloads/5o7h.pdb

5o7h.pdb title:  
Structure of the cascade-I-FV complex from shewanella putrefaciens [more
info...]  
  
Chain information for 5o7h.pdb #1  
---  
Chain | Description | UniProt  
A | CRRNA |  
B | crispr-associated protein, CSY4 family | A4Y6G3_SHEPC  
C D E | CAS7FV | A4Y6G1_SHEPC  
F | CAS5FV | A4Y6G2_SHEPC  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 12262 atom radii, 12563 bond radii, 5 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 5o7h.pdb #1  
---  
warnings | Not adding hydrogens to /A C 1 P because it is missing heavy-atom
bond partners  
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it  
notes | Termini for 5o7h.pdb (#1) chain A determined from SEQRES records  
Termini for 5o7h.pdb (#1) chain B determined from SEQRES records  
Termini for 5o7h.pdb (#1) chain C determined from SEQRES records  
Termini for 5o7h.pdb (#1) chain D determined from SEQRES records  
Termini for 5o7h.pdb (#1) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /B MSE 15, /D MSE 1, /F MSE
1  
Chain-initial residues that are not actual N termini: /B GLN 93, /B GLU 168,
/C GLN 2, /C ASP 39, /C LEU 105, /C LYS 163, /E GLN 2  
Chain-final residues that are actual C termini: /B PRO 181, /C LYS 315, /D LYS
315, /F LEU 336  
Chain-final residues that are not actual C termini: /B ASP 60, /B GLN 161, /C
THR 31, /C GLU 92, /C ASN 145, /E TYR 313  
Missing OXT added to C-terminal residue /B PRO 181  
Missing OXT added to C-terminal residue /C LYS 315  
Missing OXT added to C-terminal residue /D LYS 315  
Missing OXT added to C-terminal residue /F LEU 336  
1263 hydrogen bonds  
Adding 'H' to /B GLN 93  
Adding 'H' to /B GLU 168  
Adding 'H' to /C GLN 2  
Adding 'H' to /C ASP 39  
Adding 'H' to /C LEU 105  
2 messages similar to the above omitted  
/E TYR 313 is not terminus, removing H atom from 'C'  
10897 hydrogens added  
  

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A C 43  

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen /A C 43 H5' bonded to atom that should not have hydrogens (/A C 43
O5')  

> close session

> open 1M6X

Summary of feedback from opening 1M6X fetched from pdb  
---  
notes | Fetching compressed mmCIF 1m6x from
http://files.rcsb.org/download/1m6x.cif  
Fetching CCD PTR from http://ligand-expo.rcsb.org/reports/P/PTR/PTR.cif  
  
1m6x title:  
Flpe-Holliday Junction Complex [more info...]  
  
Chain information for 1m6x #1  
---  
Chain | Description | UniProt  
A B | Flp recombinase | FLP_YEAST  
C D | Flp recombinase | FLP_YEAST  
E F | Symmetrized FRT site |  
G H | Symmetrized FRT site |  
I J | Symmetrized FRT site |  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 15641 atom radii, 16241 bond radii, 14 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 1m6x #1  
---  
warning | Not adding hydrogens to /G DT 1 C5' because it is missing heavy-atom
bond partners  
notes | Termini for 1m6x (#1) chain E determined from SEQRES records  
Termini for 1m6x (#1) chain I determined from SEQRES records  
Termini for 1m6x (#1) chain F determined from SEQRES records  
Termini for 1m6x (#1) chain J determined from SEQRES records  
Termini for 1m6x (#1) chain G determined from SEQRES records  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A SER 2, /A SER 114, /A
GLY 136, /A GLN 346, /B SER 2, /B SER 114, /B GLY 136, /B TYR 343, /C SER 2,
/C SER 114, /C ASN 137, /C ASN 268, /C GLU 395, /D SER 2, /D SER 114, /D ASN
137, /D LYS 269, /D GLU 395  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLY 109, /A SER 129, /A
LYS 333, /A ARG 422, /B GLY 109, /B SER 129, /B ASP 332, /B ARG 422, /C ASN
108, /C SER 129, /C GLY 263, /C GLN 389, /C ARG 422, /D ASN 108, /D SER 129,
/D ASN 264, /D GLN 389, /D ARG 422  
1775 hydrogen bonds  
Adding 'H' to /A SER 2  
Adding 'H' to /A SER 114  
Adding 'H' to /A GLY 136  
Adding 'H' to /A GLN 346  
Adding 'H' to /B SER 2  
13 messages similar to the above omitted  
/A ARG 422 is not terminus, removing H atom from 'C'  
/B ARG 422 is not terminus, removing H atom from 'C'  
/C ARG 422 is not terminus, removing H atom from 'C'  
/D ARG 422 is not terminus, removing H atom from 'C'  
/I DT 32 is not terminus, removing H atom from O3'  
14630 hydrogens added  
  

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/G DT 1  
/G DC 33  
/H DC 33  
/J DC 33  

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen /H DC 33 H5' bonded to atom that should not have hydrogens (/H DC 33
O5')  

> close session

> open pubchem:9238

Summary of feedback from opening 9238 fetched from pubchem  
---  
note | Fetching compressed PubChem 9238 from
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/9238/SDF?record_type=3d  
  
Number of charges (1) in PUBCHEM_MMFF94_PARTIAL_CHARGES data not equal to
number of atoms (26)  

> close session

> open C:/Users/brownekm/Downloads/4gfh.pdb

4gfh.pdb title:  
Topoisomerase II-DNA-amppnp complex [more info...]  
  
Chain information for 4gfh.pdb #1  
---  
Chain | Description | UniProt  
A | DNA topoisomerase II | TOP2_YEAST  
B G | DNA (5'-D(P*CP*CP*TP*ap*CP*TP*GP*CP*TP*ap*C)-3') |  
C H | DNA (5'-D(*CP*GP*CP*GP*GP*TP*ap*GP*CP*ap*GP*TP*ap*GP*G)- 3') |  
D I | DNA (5'-D(P*GP*GP*ap*TP*GP*ap*CP*GP*ap*TP*(TSP))-3') |  
E J | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*CP*GP*TP*CP*ap*TP*CP*C)- 3') |  
F | DNA topoisomerase II | TOP2_YEAST  
  
Non-standard residues in 4gfh.pdb #1  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
TSP — 3'-thio-thymidine-5'-phosphate  
  

> preset nih3d "surface hydrophobicity"

Using preset: NIH3D / Surface Hydrophobicity  
Changed 20236 atom radii, 20880 bond radii, 16 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 4gfh.pdb #1  
---  
warnings | Not adding hydrogens to /B DC 1 P (alt loc A) because it is missing
heavy-atom bond partners  
Not adding hydrogens to /C DC 1 C5' (alt loc A) because it is missing heavy-
atom bond partners  
Not adding hydrogens to /D DG 1 P (alt loc B) because it is missing heavy-atom
bond partners  
Not adding hydrogens to /G DC 1 P (alt loc A) because it is missing heavy-atom
bond partners  
Not adding hydrogens to /H DC 1 C5' (alt loc A) because it is missing heavy-
atom bond partners  
1 messages similar to the above omitted  
Skipped 10 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for 4gfh.pdb (#1) chain A; guessing termini
instead  
Termini for 4gfh.pdb (#1) chain B determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain C determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain D determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain E determined from SEQRES records  
No usable SEQRES records for 4gfh.pdb (#1) chain F; guessing termini instead  
Termini for 4gfh.pdb (#1) chain G determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain H determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain I determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain J determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 7, /F SER 7, /A SER
7, /A ILE 276, /A SER 421, /A THR 607, /A GLU 1107, /F SER 7, /F ILE 276, /F
SER 421, /F THR 607, /F GLU 1107  
Chain-initial residues that are not actual N termini: /A ILE 276, /A SER 421,
/A THR 607, /A GLU 1107, /F ILE 276, /F SER 421, /F THR 607, /F GLU 1107  
Chain-final residues that are actual C termini: /A LEU 258, /A GLU 408, /A TYR
602, /A SER 1070, /A ARG 1177, /F LEU 258, /F ALA 404, /F TYR 602, /F SER
1070, /F ARG 1177  
Chain-final residues that are not actual C termini: /A ARG 1177, /A LEU 258,
/A GLU 408, /A TYR 602, /A SER 1070, /F ARG 1177, /F LEU 258, /F ALA 404, /F
TYR 602, /F SER 1070  
Missing OXT added to C-terminal residue /A LEU 258  
Missing OXT added to C-terminal residue /A GLU 408  
Missing OXT added to C-terminal residue /A TYR 602  
Missing OXT added to C-terminal residue /A SER 1070  
Missing OXT added to C-terminal residue /A ARG 1177  
5 messages similar to the above omitted  
Skipping possible acceptor with bad geometry: /F PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /F PTR 782 O (alt loc A)  
  
Skipping possible acceptor with bad geometry: /A PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /A PTR 782 O (alt loc A)  
  
Skipping possible acceptor with bad geometry: /A PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /A PTR 782 O (alt loc A)  
  
Skipping possible acceptor with bad geometry: /F PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /F PTR 782 O (alt loc A)  
  
Skipping possible acceptor with bad geometry: /A PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /A PTR 782 O (alt loc A)  
  
5 messages similar to the above omitted  
2199 hydrogen bonds  
Adding 'H' to /A ILE 276  
Adding 'H' to /A SER 421  
Adding 'H' to /A THR 607  
Adding 'H' to /A GLU 1107  
Adding 'H' to /F ILE 276  
3 messages similar to the above omitted  
19345 hydrogens added  
  
2202 residues, 1 surfaces, atom kd_hydrophobicity range -4.5 to 4.5  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1
    surface #1 enclose #1 grid 1.80612 sharp true
    color magenta
    color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 39591 atom radii, 40235 bond radii, 16 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.  

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/H DC 1 O5'  
/C DC 1 O5'  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PTR (net charge -1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpmh8mzxba\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpmh8mzxba\ante.out.mol2 -fo mol2 -c
bcc -nc -1 -j 5 -s 2 -dr n  
(PTR) ``  
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`  
(PTR) ``  
(PTR) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpmh8mzxba\ante.in.mol2); atoms read
(47), bonds read (47).`  
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PTR) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PTR) `bash.exe: warning: could not find /tmp, please create!`  
(PTR) ``  
(PTR) ``  
(PTR) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PTR) `bash.exe: warning: could not find /tmp, please create!`  
(PTR) `Info: Total number of electrons: 204; net charge: -1`  
(PTR) ``  
(PTR) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(PTR) `bash.exe: warning: could not find /tmp, please create!`  
(PTR) `/usr/bin/antechamber: Fatal Error!`  
(PTR) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue PTR  
Check reply log for details  

> close session

> open pubchem:9238

Number of charges (1) in PUBCHEM_MMFF94_PARTIAL_CHARGES data not equal to
number of atoms (26)  

> open C:\Users\brownekm\Downloads\4gfh.pdb format pdb

4gfh.pdb title:  
Topoisomerase II-DNA-amppnp complex [more info...]  
  
Chain information for 4gfh.pdb #1  
---  
Chain | Description | UniProt  
A | DNA topoisomerase II | TOP2_YEAST  
B G | DNA (5'-D(P*CP*CP*TP*ap*CP*TP*GP*CP*TP*ap*C)-3') |  
C H | DNA (5'-D(*CP*GP*CP*GP*GP*TP*ap*GP*CP*ap*GP*TP*ap*GP*G)- 3') |  
D I | DNA (5'-D(P*GP*GP*ap*TP*GP*ap*CP*GP*ap*TP*(TSP))-3') |  
E J | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*CP*GP*TP*CP*ap*TP*CP*C)- 3') |  
F | DNA topoisomerase II | TOP2_YEAST  
  
Non-standard residues in 4gfh.pdb #1  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
TSP — 3'-thio-thymidine-5'-phosphate  
  

> close session

> open C:\Users\brownekm\Downloads\4gfh.pdb format pdb

4gfh.pdb title:  
Topoisomerase II-DNA-amppnp complex [more info...]  
  
Chain information for 4gfh.pdb #1  
---  
Chain | Description | UniProt  
A | DNA topoisomerase II | TOP2_YEAST  
B G | DNA (5'-D(P*CP*CP*TP*ap*CP*TP*GP*CP*TP*ap*C)-3') |  
C H | DNA (5'-D(*CP*GP*CP*GP*GP*TP*ap*GP*CP*ap*GP*TP*ap*GP*G)- 3') |  
D I | DNA (5'-D(P*GP*GP*ap*TP*GP*ap*CP*GP*ap*TP*(TSP))-3') |  
E J | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*CP*GP*TP*CP*ap*TP*CP*C)- 3') |  
F | DNA topoisomerase II | TOP2_YEAST  
  
Non-standard residues in 4gfh.pdb #1  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
TSP — 3'-thio-thymidine-5'-phosphate  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 20236 atom radii, 20880 bond radii, 16 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 4gfh.pdb #1  
---  
warnings | Not adding hydrogens to /B DC 1 P (alt loc A) because it is missing
heavy-atom bond partners  
Not adding hydrogens to /C DC 1 C5' (alt loc A) because it is missing heavy-
atom bond partners  
Not adding hydrogens to /D DG 1 P (alt loc B) because it is missing heavy-atom
bond partners  
Not adding hydrogens to /G DC 1 P (alt loc A) because it is missing heavy-atom
bond partners  
Not adding hydrogens to /H DC 1 C5' (alt loc A) because it is missing heavy-
atom bond partners  
1 messages similar to the above omitted  
Skipped 10 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for 4gfh.pdb (#1) chain A; guessing termini
instead  
Termini for 4gfh.pdb (#1) chain B determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain C determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain D determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain E determined from SEQRES records  
No usable SEQRES records for 4gfh.pdb (#1) chain F; guessing termini instead  
Termini for 4gfh.pdb (#1) chain G determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain H determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain I determined from SEQRES records  
Termini for 4gfh.pdb (#1) chain J determined from SEQRES records  
Chain-initial residues that are actual N termini: /A SER 7, /F SER 7, /A SER
7, /A ILE 276, /A SER 421, /A THR 607, /A GLU 1107, /F SER 7, /F ILE 276, /F
SER 421, /F THR 607, /F GLU 1107  
Chain-initial residues that are not actual N termini: /A ILE 276, /A SER 421,
/A THR 607, /A GLU 1107, /F ILE 276, /F SER 421, /F THR 607, /F GLU 1107  
Chain-final residues that are actual C termini: /A LEU 258, /A GLU 408, /A TYR
602, /A SER 1070, /A ARG 1177, /F LEU 258, /F ALA 404, /F TYR 602, /F SER
1070, /F ARG 1177  
Chain-final residues that are not actual C termini: /A ARG 1177, /A LEU 258,
/A GLU 408, /A TYR 602, /A SER 1070, /F ARG 1177, /F LEU 258, /F ALA 404, /F
TYR 602, /F SER 1070  
Missing OXT added to C-terminal residue /A LEU 258  
Missing OXT added to C-terminal residue /A GLU 408  
Missing OXT added to C-terminal residue /A TYR 602  
Missing OXT added to C-terminal residue /A SER 1070  
Missing OXT added to C-terminal residue /A ARG 1177  
5 messages similar to the above omitted  
Skipping possible acceptor with bad geometry: /F PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /F PTR 782 O (alt loc A)  
  
Skipping possible acceptor with bad geometry: /A PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /A PTR 782 O (alt loc A)  
  
Skipping possible acceptor with bad geometry: /A PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /A PTR 782 O (alt loc A)  
  
Skipping possible acceptor with bad geometry: /F PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /F PTR 782 O (alt loc A)  
  
Skipping possible acceptor with bad geometry: /A PTR 782 O (alt loc A)  
Wrong number of grandchild atoms for phi/psi acceptor /A PTR 782 O (alt loc A)  
  
5 messages similar to the above omitted  
2199 hydrogen bonds  
Adding 'H' to /A ILE 276  
Adding 'H' to /A SER 421  
Adding 'H' to /A THR 607  
Adding 'H' to /A GLU 1107  
Adding 'H' to /F ILE 276  
3 messages similar to the above omitted  
19345 hydrogens added  
  

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/H DC 1 O5'  
/C DC 1 O5'  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PTR (net charge -1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\brownekm\AppData\Local\Temp\1\tmpa8bpxjvh\ante.in.mol2 -fi mol2 -o
C:\Users\brownekm\AppData\Local\Temp\1\tmpa8bpxjvh\ante.out.mol2 -fo mol2 -c
bcc -nc -1 -j 5 -s 2 -dr n  
(PTR) ``  
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`  
(PTR) ``  
(PTR) `Info: Finished reading file
(C:\Users\brownekm\AppData\Local\Temp\1\tmpa8bpxjvh\ante.in.mol2); atoms read
(47), bonds read (47).`  
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PTR) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PTR) `bash.exe: warning: could not find /tmp, please create!`  
(PTR) ``  
(PTR) ``  
(PTR) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PTR) `bash.exe: warning: could not find /tmp, please create!`  
(PTR) `Info: Total number of electrons: 204; net charge: -1`  
(PTR) ``  
(PTR) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(PTR) `bash.exe: warning: could not find /tmp, please create!`  
(PTR) `/usr/bin/antechamber: Fatal Error!`  
(PTR) `Cannot properly run ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue PTR  
Check reply log for details  

> close session

> open C:/Users/brownekm/Downloads/3ZG6-SIRT6.pdb

Summary of feedback from opening C:/Users/brownekm/Downloads/3ZG6-SIRT6.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Accelrys Discovery Studio PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2017-07-20T20:58:54Z  
  
Chain information for 3ZG6-SIRT6.pdb #1  
---  
Chain | Description  
A | No description available  
F | No description available  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 4905 atom radii, 4961 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 3ZG6-SIRT6.pdb #1  
---  
warnings | Both O and OXT missing from C-terminal residue /A LYS 294; cannot
complete teminus  
Both O and OXT missing from C-terminal residue /F TRP 15; cannot complete
teminus  
notes | No usable SEQRES records for 3ZG6-SIRT6.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for 3ZG6-SIRT6.pdb (#1) chain F; guessing termini
instead  
Chain-initial residues that are actual N termini: /A MET 1, /F LYS 4  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 294, /F TRP 15  
Chain-final residues that are not actual C termini:  
290 hydrogen bonds  
3 hydrogens added  
  

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/F TRP 15 O  
/A LYS 294 O  

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /F TRP 15 1OCT  




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

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

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

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.43.2
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202210260016
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.25
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.5
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.10.0
File attachment: 3ZG6-SIRT6.pdb

3ZG6-SIRT6.pdb​

Attachments (1)

3ZG6-SIRT6.pdb​ (390.8 KB ) - added by kristen.browne@… 3 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (7)

by kristen.browne@…, 3 years ago

Attachment: 3ZG6-SIRT6.pdb​ added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → non-standard C-terminal oxygen name

comment:2 by Eric Pettersen, 3 years ago

C-terminal oxygens named 1OCT and 2OCT

comment:3 by Eric Pettersen, 3 years ago

Cc: phil.cruz@… michal.stolarczyk@… added
Status: accepted → feedback

For atoms with wonky non-standard names like this, Chimera would treat their charge as zero and assign no GAFF type and then soldier on, frequently producing an error in the downstream calculation (e.g. minimization) but producing some kind of result for something like coulombic (with varying degrees of inaccuracy). ChimeraX does not soldier on -- it stops so that the user is not blithely unaware that there is a problem.

The error that gets thrown when charging fails is ChargeError. The part of the NIH3D script that calls the coulombic preset could catch ChargeError and do whatever is appropriate (notify the user, continue on to the next preset, etc.). Opinions?

comment:4 by Eric Pettersen, 3 years ago

Belay that. ChargeError gets caught before it would reach the script so that won't work. I'll if I can get this 1OCT/2OCT situation to work without script changes.

in reply to:  6 comment:5 by kristen.browne@…, 3 years ago 

Ideally, what we like to happen under any circumstance where a preset fails would be:
1) Move on to the next preset (don't just crash out if the others are working fine)
2) Relay an informative error message that includes: a) The preset that failed and b) The error code associated with the failure.

That way we can still let them publish what WAS successful and let them know why the one preset might have failed.  Sometimes it will just be their wonky files, sometimes it might be something we want to report to you guys and have fixed.  If 2) is in place then we can generate a file on our end that the API  can parse into something displayed to the user and findable by admins.



-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, November 15, 2022 12:22 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; Stolarczyk, Michal (NIH/NIAID) [C] <michal.stolarczyk@nih.gov>; pett@cgl.ucsf.edu; Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #8029: non-standard C-terminal oxygen name

#8029: non-standard C-terminal oxygen name
----------------------------------------+----------------------
          Reporter:  kristen.browne@...   |      Owner:  pett
              Type:  defect             |     Status:  feedback
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------

Comment (by pett):

 Belay that.  ChargeError gets caught before it would reach the script so  that won't work.  I'll if I can get this 1OCT/2OCT situation to work  without script changes.

--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8029%23comment%3A4&amp;data=05%7C01%7Ckristen.browne%40nih.gov%7Ccc49f8d73b8243b9ee2108dac72dee4c%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638041297333036034%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=KYBp5fp3TcmcxuRooJgIScr7lgKjid7vmhgLDS8IeN4%3D&amp;reserved=0>
ChimeraX <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=05%7C01%7Ckristen.browne%40nih.gov%7Ccc49f8d73b8243b9ee2108dac72dee4c%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638041297333036034%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=9hsUbqU2y0l%2BM8YJS3NLlqTZth460DjED8scXGQ8JkQ%3D&amp;reserved=0>
ChimeraX Issue Tracker
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

comment:6 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: feedback → closed

Add Charge will allow 1OCT and 2OCT as C-terminal oxygen names starting with tomorrow's daily build.

fix: ​https://github.com/RBVI/ChimeraX/commit/3bc935d6611fe2708354c747acbb55894b7b1894

Note: See TracTickets for help on using tickets.