Opened 3 years ago

Closed 3 years ago

#8031 closed defect (not a bug)

Incorrect element column in PDB file

Reported by: kristen.browne@… Owned by: pett
Priority: normal Milestone:
Component: Input/Output 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 of coulombic surface
Hydrogen /? PRO 5 CB not bonded to exactly one other atom
https://3dprint.nih.gov/discover/3DPX-009046
Maybe related to issue #8023 but not sure.

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  

> close session

> open C:/Users/brownekm/Downloads/MARCpeptide.mol2

Chain information for ***** #1  
---  
Chain | Description  
? | No description available  
  
Opened MARCpeptide.mol2 containing 1 structures (130 atoms, 128 bonds)  

> preset nih3d cpk

Using preset: NIH3D / CPK  
Changed 130 atom radii, 128 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Changed 130 atom styles  
Changed 68 atom radii  
Changed 0 atom radii  
Changed 128 bond radii  
Changed 0 pseudobond dashes  
Changed 0 pseudobond radii  
Changed 0 atom radii  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    color jmol_carbon
    color byhet
    style sphere
    ~nuc
    ~ribbon
    disp
    size H atomRadius 1.1
    size ions atomRadius +0.35
    size stickRadius 0.8
    style dashes 0
    size pseudobondRadius 0.4
    size ions atomRadius +0.35

  

> preset nih3d "cpk monochrome"

Using preset: NIH3D / CPK Monochrome  
Changed 130 atom radii, 128 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Changed 130 atom styles  
Changed 68 atom radii  
Changed 0 atom radii  
Changed 128 bond radii  
Changed 0 pseudobond dashes  
Changed 0 pseudobond radii  
Changed 0 atom radii  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    style sphere
    ~nuc
    ~ribbon
    disp
    color nih_blue
    size H atomRadius 1.1
    size ions atomRadius +0.35
    size stickRadius 0.8
    style dashes 0
    size pseudobondRadius 0.4
    size ions atomRadius +0.35

  

> preset nih3d sticks

Using preset: NIH3D / Sticks  
Changed 130 atom radii, 128 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Changed 130 atom styles  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    color jmol_carbon
    color byhet
    style stick
    ~nuc
    ~ribbon
    disp

  

> preset nih3d "sticks (printable)"

Using preset: NIH3D / Sticks (Printable)  
Changed 130 atom radii, 128 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Changed 130 atom styles  
Changed 128 bond radii  
Changed 0 pseudobond dashes  
Changed 0 pseudobond radii  
Changed 0 atom radii  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    color jmol_carbon
    color byhet
    style stick
    ~nuc
    ~ribbon
    disp
    size stickRadius 0.8
    style dashes 0
    size pseudobondRadius 0.4
    size ions atomRadius +0.35

  

> preset nih3d "sticks monochrome (printable)"

Using preset: NIH3D / Sticks Monochrome (Printable)  
Changed 130 atom radii, 128 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Changed 130 atom styles  
Changed 128 bond radii  
Changed 0 pseudobond dashes  
Changed 0 pseudobond radii  
Changed 0 atom radii  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    style stick
    ~nuc
    ~ribbon
    disp
    color nih_blue
    size stickRadius 0.8
    style dashes 0
    size pseudobondRadius 0.4
    size ions atomRadius +0.35

  

> preset nih3d sticks

Using preset: NIH3D / Sticks  
Changed 130 atom radii, 128 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Changed 130 atom styles  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    color jmol_carbon
    color byhet
    style stick
    ~nuc
    ~ribbon
    disp

  

> close session

> open C:/Users/brownekm/Downloads/3HBut-coA.PDB

Summary of feedback from opening C:/Users/brownekm/Downloads/3HBut-coA.PDB  
---  
warnings | Ignored bad PDB record found on line 1  
3HC  
  
Ignored bad PDB record found on line 2  
-ISIS- 3D  
  
Ignored bad PDB record found on line 3  
  
  
Ignored bad PDB record found on line 4  
96 98 0 0 0 0 0 0 0 0 0  
  
Ignored bad PDB record found on line 5  
4.9120 1.4210 -11.4810 N 0 0 0 0 0  
  
195 messages similar to the above omitted  
  

> open C:\Users\brownekm\Downloads\3HBut-coA.PDB format pdb

Summary of feedback from opening C:\Users\brownekm\Downloads\3HBut-coA.PDB  
---  
warnings | Ignored bad PDB record found on line 1  
3HC  
  
Ignored bad PDB record found on line 2  
-ISIS- 3D  
  
Ignored bad PDB record found on line 3  
  
  
Ignored bad PDB record found on line 4  
96 98 0 0 0 0 0 0 0 0 0  
  
Ignored bad PDB record found on line 5  
4.9120 1.4210 -11.4810 N 0 0 0 0 0  
  
195 messages similar to the above omitted  
  

> open pubchem:66348

Summary of feedback from opening 66348 fetched from pubchem  
---  
note | Fetching compressed PubChem 66348 from
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/66348/SDF?record_type=3d  
  
Number of charges (1) in PUBCHEM_MMFF94_PARTIAL_CHARGES data not equal to
number of atoms (8)  

> open "C:/Users/brownekm/Downloads/2.5F phyre prediction.pdb"

Chain information for 2.5F phyre prediction.pdb #1  
---  
Chain | Description  
? | No description available  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 241 atom radii, 246 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 2.5F phyre prediction.pdb #1  
---  
warnings | Not adding hydrogens to /? PRO 5 CA because it is missing heavy-
atom bond partners  
Not adding hydrogens to /? PRO 5 CG because it is missing heavy-atom bond
partners  
Unknown hybridization for atoms (HE22, HE21) of residue type GLN; not adding
hydrogens to them  
notes | No usable SEQRES records for 2.5F phyre prediction.pdb (#1) chain
(blank); guessing termini instead  
Chain-initial residues that are actual N termini: /? GLY 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /? GLY 33  
Chain-final residues that are not actual C termini:  
21 hydrogen bonds  
186 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen /? PRO 5 CB not bonded to exactly one other atom  




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

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File attachment: 2.5F phyre prediction.pdb

2.5F phyre prediction.pdb​

Attachments (1)

2.5F phyre prediction.pdb​ (19.3 KB ) - added by kristen.browne@… 3 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by kristen.browne@…, 3 years ago

Attachment: 2.5F phyre prediction.pdb​ added

Added by email2trac

comment:1 by pett, 3 years ago

Component: Unassigned → Input/Output
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Incorrect element column in PDB file

comment:2 by pett, 3 years ago

Resolution: → not a bug
Status: accepted → closed

The input PDB file is just bad. The "element' column is *mostly* the proper chemical symbols, but many are not (e.g. "N1+"). The topper is that the element for CB in PRO5 is "H"! At any rate, the pull request I made for the other ticket will also skip coulombic for this problematic structure.

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