Opened 3 years ago

Closed 3 years ago

#7674 closed defect (fixed)

Report sqm.out; try to make quotes "reusable"

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Failures in adding charges are currently really difficult for even the moderately savvy user to debug, for a few reasons:

- when SQM fails, the relevant error messages are written to sqm.out rather than stdout/stderr. Since sqm.out is deleted along with the temporary directory, that's all lost.
- in the logged command (i.e.: "Running ANTECHAMBER command: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.in.mol2 -fi mol2 -o /var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.out.mol2 -fo mol2 -c bcc -nc -5 -j 5 -s 2 -dr n") the quotes around 'AM1' are not the same unicode symbol as the quotes expected by antechamber - so if I copy/paste/modify the command to the shell, the result is an inscrutable error message:


Fortran runtime error: Cannot match namelist object name am1 

... which goes away if I delete and re-type the quotes on the command line.

I think it would be much better if the ChimeraX code could capture and report the sqm.out contents (if they exist) on failure.



Log:
Startup Messages  
---  
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7pqd

Summary of feedback from opening 7pqd fetched from pdb  
---  
notes | Fetching compressed mmCIF 7pqd from
http://files.rcsb.org/download/7pqd.cif  
Fetching CCD BCL from http://ligand-expo.rcsb.org/reports/B/BCL/BCL.cif  
Fetching CCD SP2 from http://ligand-expo.rcsb.org/reports/S/SP2/SP2.cif  
Fetching CCD 3PE from http://ligand-expo.rcsb.org/reports/3/3PE/3PE.cif  
Fetching CCD CD4 from http://ligand-expo.rcsb.org/reports/C/CD4/CD4.cif  
Fetching CCD UQ1 from http://ligand-expo.rcsb.org/reports/U/UQ1/UQ1.cif  
Fetching CCD U10 from http://ligand-expo.rcsb.org/reports/U/U10/U10.cif  
Fetching CCD BPH from http://ligand-expo.rcsb.org/reports/B/BPH/BPH.cif  
Fetching CCD SQD from http://ligand-expo.rcsb.org/reports/S/SQD/SQD.cif  
Fetching CCD LMT from http://ligand-expo.rcsb.org/reports/L/LMT/LMT.cif  
Fetching CCD FE from http://ligand-expo.rcsb.org/reports/F/FE/FE.cif  
Fetching CCD FME from http://ligand-expo.rcsb.org/reports/F/FME/FME.cif  
  
7pqd title:  
Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex
at 2.9 A: the structural basis for dimerisation [more info...]  
  
Chain information for 7pqd #1  
---  
Chain | Description | UniProt  
AA AB AC AD AE AF AG AH AI AJ AK AL AM AN aa ab ac ad ae af ag ah ai aj ak al
am an | LH1-alpha |  
BA BB BC BD BE BF BG BH BI BJ BK BL BM BN ba bb bc bd be bf bg bh bi bj bk bl
bm bn | LH1-beta |  
H h | RC-H |  
L l | RC-L |  
M m | Reaction center protein M chain | RCEM_RHOS4  
UA UB ua ub | PufZ |  
UU uu | PufY |  
X x | PufX |  
  
Non-standard residues in 7pqd #1  
---  
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)  
BCL — bacteriochlorophyll A  
BPH — bacteriopheophytin A  
CD4 —
(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl
tetradecanoate (tetramyristoyl-cardiolipin)  
FE — Fe (III) ion  
LMT — dodecyl-β-D-maltoside  
SP2 — 3,4-dihydrospheroidene  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
U10 — ubiquinone-10 (Coenzyme Q10)  
UQ1 — ubiquinone-1  
  

> usage vol

volume [volumes] [style style] [change change] [show] [hide] [toggle] [close
close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume
encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness
a number] [transparency a number] [appearance appearance] [nameAppearance a
text string] [nameForget nameForget] [step map step] [region map region]
[expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3
floats] [voxelSize 1 or 3 floats] [planes planes
x|y|z[,<start>[,<end>[,<increment>[,<depth>]]]]] [dumpHeader true or false]
[pickable true or false] [symmetry symmetry] [center center point]
[centerIndex 1 or 3 floats] [axis an axis vector] [coordinateSystem a
coordinate-system] [dataCacheSize a number] [showOnOpen true or false]
[voxelLimitForOpen a number] [showPlane true or false] [voxelLimitForPlane a
number] [showOutlineBox true or false] [outlineBoxRgb a color]
[limitVoxelCount true or false] [voxelLimit a number] [colorMode colorMode]
[colormapOnGpu true or false] [colormapSize an integer] [colormapExtendLeft
true or false] [colormapExtendRight true or false] [backingColor backingColor]
[blendOnGpu true or false] [projectionMode projectionMode] [planeSpacing
planeSpacing] [fullRegionOnGpu true or false] [btCorrection true or false]
[minimalTextureMemory true or false] [maximumIntensityProjection true or
false] [linearInterpolation true or false] [dimTransparency true or false]
[dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
true or false] [twoSidedLighting true or false] [flipNormals true or false]
[subdivideSurface true or false] [subdivisionLevels an integer]
[surfaceSmoothing true or false] [smoothingIterations an integer]
[smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
[boxFaces true or false] [orthoplanes orthoplanes] [positionPlanes
positionPlanes] [tiltedSlab true or false] [tiltedSlabAxis an axis vector]
[tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount
an integer] [imageMode imageMode] [calculateSurfaces true or false]  
— set volume model parameters, display style and colors  
style: one of image, mesh, solid, or surface  
change: one of image or surface  
close: one of image or surface  
level: some numbers, repeatable  
rmsLevel: some numbers, repeatable  
sdLevel: some numbers, repeatable  
encloseVolume: some numbers  
fastEncloseVolume: some numbers  
color: a color, repeatable  
appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin,
Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
Bone  
nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin,
Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs,
CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone,
Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid
Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II,
Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on
White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow
Bone  
colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
rgba12, rgba16, rgba4, or rgba8  
backingColor: a color or none  
projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, or auto  
planeSpacing: one of max, mean, or min or a number  
orthoplanes: one of off, xy, xyz, xz, or yz  
positionPlanes: some integers  
imageMode: one of box faces, full region, orthoplanes, or tilted slab  
Subcommands are:

  * volume add
  * volume bin
  * volume boxes
  * volume channels
  * volume copy
  * volume cover
  * volume erase
  * volume falloff
  * volume flatten
  * volume flip
  * volume fourier
  * volume gaussian
  * volume laplacian
  * volume localCorrelation
  * volume mask
  * volume maximum
  * volume median
  * volume minimum
  * volume morph
  * volume multiply
  * volume new
  * volume octant
  * volume ~octant
  * volume onesmask
  * volume permuteAxes
  * volume resample
  * volume ridges
  * volume scale
  * volume settings
  * volume splitbyzone
  * volume subtract
  * volume threshold
  * volume tile
  * volume unbend
  * volume unroll
  * volume unzone
  * volume zone

  

> usage mol

molmap atoms resolution [gridSpacing gridSpacing] [edgePadding a number]
[onGrid a density map specifier] [cutoffRange a number] [sigmaFactor a number]
[balls true or false] [symmetry symmetry] [center center point] [axis an axis
vector] [coordinateSystem a coordinate-system] [displayThreshold a number]
[replace true or false] [showDialog true or false]  
— Compute a map by placing Gaussians at atom positions  
resolution: a number > 0  
gridSpacing: a number > 0  

> molmap #1 3

Opened 7pqd map 3 as #2, grid size 152,233,113, pixel 1, shown at level 0.11,
step 1, values float32  

> hide #!1 models

> volume invert \2

Expected a density maps specifier or a keyword  

> volume invert #2

Expected a density maps specifier or a keyword  

> volume multiply #2 -1

Expected a keyword  

> volume multiply -1 #2

Missing or invalid "volumes" argument: invalid density maps specifier  

> usage vol mult

volume multiply volumes [onGrid a density maps specifier] [boundingGrid true
or false] [gridSubregion map region] [gridStep map step] [spacing 1 or 3
floats] [valueType numeric value type] [hideMaps true or false] [subregion map
region] [step map step] [modelId modelId] [inPlace true or false]
[scaleFactors scaleFactors]  
— Multiply maps pointwise  
modelId: a model id  
scaleFactors: some numbers  

> volume scale #2 factor -1

Opened 7pqd map 3 scaled as #3, grid size 152,233,113, pixel 1, shown at step
1, values float32  

> volume #3 level -0.8116

> volume #3 level -0.7766

> ui tool show "Side View"

> close #3

> ui tool show "Side View"

> lighting soft

> close #2

> show #!1 models

> molmap #1 res 3

Missing or invalid "resolution" argument: Expected a number  

> molmap #1 3

Opened 7pqd map 3 as #2, grid size 152,233,113, pixel 1, shown at level 0.11,
step 1, values float32  

> color #2 near 1

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #2 near #1

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #2 fromatoms #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color zone #2 near #1

> hide #!1 models

> usage molmap

molmap atoms resolution [gridSpacing gridSpacing] [edgePadding a number]
[onGrid a density map specifier] [cutoffRange a number] [sigmaFactor a number]
[balls true or false] [symmetry symmetry] [center center point] [axis an axis
vector] [coordinateSystem a coordinate-system] [displayThreshold a number]
[replace true or false] [showDialog true or false]  
— Compute a map by placing Gaussians at atom positions  
resolution: a number > 0  
gridSpacing: a number > 0  

> close #2

> molmap #1 6

Opened 7pqd map 6 as #2, grid size 85,126,66, pixel 2, shown at level 0.109,
step 1, values float32  

> color zone #2 near #1

> color zone #2 near #1 range 5

Expected a keyword  

> color zone #2 near #1 distance 5

> show #!1 models

> hide #!2 models

> cartoon

> hide protein

> molmap #1&(protein|:BCL,SP2,HEM,HEC) 5

Opened 7pqd map 5 as #3, grid size 99,147,75, pixel 1.67, shown at level
0.104, step 1, values float32  

> close #2

> close #1,3

> open 5xth

Summary of feedback from opening 5xth fetched from pdb  
---  
notes | Fetching compressed mmCIF 5xth from
http://files.rcsb.org/download/5xth.cif  
Fetching CCD PLX from http://ligand-expo.rcsb.org/reports/P/PLX/PLX.cif  
Fetching CCD 8Q1 from http://ligand-expo.rcsb.org/reports/8/8Q1/8Q1.cif  
Fetching CCD NDP from http://ligand-expo.rcsb.org/reports/N/NDP/NDP.cif  
Fetching CCD CDL from http://ligand-expo.rcsb.org/reports/C/CDL/CDL.cif  
Fetching CCD PEE from http://ligand-expo.rcsb.org/reports/P/PEE/PEE.cif  
Fetching CCD CU from http://ligand-expo.rcsb.org/reports/C/CU/CU.cif  
Fetching CCD HEA from http://ligand-expo.rcsb.org/reports/H/HEA/HEA.cif  
Fetching CCD HEC from http://ligand-expo.rcsb.org/reports/H/HEC/HEC.cif  
  
5xth title:  
Cryo-EM structure of human respiratory supercomplex I1III2IV1 [more info...]  
  
Chain information for 5xth #1  
---  
Chain | Description | UniProt  
0 | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_BOVIN  
1 | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_BOVIN  
2 | Cytochrome c oxidase subunit 5B, mitochondrial | COX5B_BOVIN  
3 | Cytochrome c oxidase subunit 6A2, mitochondrial | CX6A2_BOVIN  
4 | Cytochrome c oxidase subunit 6B1 | CX6B1_BOVIN  
5 | Cytochrome c oxidase subunit 6C | COX6C_BOVIN  
6 | Cytochrome c oxidase subunit 7A1, mitochondrial | CX7A1_BOVIN  
7 | Cytochrome c oxidase subunit 7B, mitochondrial | COX7B_BOVIN  
8 | Cytochrome c oxidase subunit 7C, mitochondrial | COX7C_BOVIN  
9 | Cytochrome c oxidase subunit 8B, mitochondrial | COX8B_BOVIN  
A | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial |
NDUV1_HUMAN  
AA AN | Cytochrome b-c1 complex subunit 8 | QCR8_HUMAN  
AB AO | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_HUMAN  
AC AP | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_HUMAN  
AD AQ | Cytochrome b-c1 complex subunit 9 | QCR9_HUMAN  
AE AR | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_HUMAN  
AF AS | Cytochrome b-c1 complex subunit 7 | QCR7_HUMAN  
AG AT | Cytochrome b-c1 complex subunit 10 | QCR10_HUMAN  
AH AU | Cytochrome c1, heme protein, mitochondrial | CY1_HUMAN  
AJ AV | Cytochrome b | CYB_HUMAN  
AK AW | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_HUMAN  
AL AY | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_HUMAN  
B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial |
NDUS8_HUMAN  
C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial |
NDUS7_HUMAN  
E | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6 | NDUA6_HUMAN  
F | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 | NDUA2_HUMAN  
G X | Acyl carrier protein, mitochondrial | ACPM_HUMAN  
H | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5 | NDUA5_HUMAN  
I | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7 | NDUA7_HUMAN  
J | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial |
NDUA9_HUMAN  
K | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial |
NDUV3_HUMAN  
L | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial |
NDUS4_HUMAN  
M | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial | NDUS1_HUMAN  
N | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12 | NDUAC_HUMAN  
O | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial |
NDUV2_HUMAN  
P | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial |
NDUS3_HUMAN  
Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial |
NDUS2_HUMAN  
S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1 | NDUA1_HUMAN  
T | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial |
NDUS6_HUMAN  
U | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3 | NDUA3_HUMAN  
V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 11 | NDUAB_HUMAN  
W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 | NDUAD_HUMAN  
Y | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial |
NDUB2_HUMAN  
Z | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3 | NDUB3_HUMAN  
a | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial |
NDUB5_HUMAN  
b | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6 | NDUB6_HUMAN  
c | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial |
NDUB8_HUMAN  
d | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10 | NDUBA_HUMAN  
e | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial |
NDUBB_HUMAN  
f | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | NDUC1_HUMAN  
g | NADH dehydrogenase [ubiquinone] 1 subunit C2 | NDUC2_HUMAN  
h | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | NDUS5_HUMAN  
i | NADH-ubiquinone oxidoreductase chain 2 | Q4GRX1_HUMAN  
j | NADH-ubiquinone oxidoreductase chain 3 | B9EE38_HUMAN  
k | NADH-ubiquinone oxidoreductase chain 4L | V9JN72_HUMAN  
l | NADH-ubiquinone oxidoreductase chain 5 | X5BVZ3_HUMAN  
m | NADH-ubiquinone oxidoreductase chain 6 | Q8HAX7_HUMAN  
n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1 | NDUB1_HUMAN  
o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4 | NDUB4_HUMAN  
p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9 | NDUB9_HUMAN  
r | NADH-ubiquinone oxidoreductase chain 4 | B2XJG5_HUMAN  
s | NADH-ubiquinone oxidoreductase chain 1 | H9PGF0_HUMAN  
u | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8 | NDUA8_HUMAN  
v | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7 | NDUB7_HUMAN  
w | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial |
NDUAA_HUMAN  
x | Cytochrome c oxidase subunit 1 | COX1_BOVIN  
y | Cytochrome c oxidase subunit 2 | COX2_BOVIN  
z | Cytochrome c oxidase subunit 3 | COX3_BOVIN  
  
Non-standard residues in 5xth #1  
---  
8Q1 — S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-
alanyl}amino)ethyl] dodecanethioate (S-dodecanoyl-4'-phosphopantetheine)  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
CU — copper (II) ion  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
HEA — heme-A  
HEC — heme C  
HEM — protoporphyrin IX containing Fe (HEME)  
MG — magnesium ion  
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate  
PEE — 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)  
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> molmap #1&(protein) 5

Opened 5xth map 5 as #2, grid size 145,188,152, pixel 1.67, shown at level
0.101, step 1, values float32  

> hide #!1 models

> show #!1 models

> cartoon

> hide

> hide #!2 models

> show #!2 models

> hide #!2 models

> show

> style stick

Changed 115642 atom styles  

> lighting simple

> close #1-2

> open 6t0b

Summary of feedback from opening 6t0b fetched from pdb  
---  
notes | Fetching compressed mmCIF 6t0b from
http://files.rcsb.org/download/6t0b.cif  
Fetching CCD PEF from http://ligand-expo.rcsb.org/reports/P/PEF/PEF.cif  
Fetching CCD PCF from http://ligand-expo.rcsb.org/reports/P/PCF/PCF.cif  
Fetching CCD CUA from http://ligand-expo.rcsb.org/reports/C/CUA/CUA.cif  
  
6t0b title:  
The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae [more info...]  
  
Chain information for 6t0b #1  
---  
Chain | Description | UniProt  
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_YEAST  
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_YEAST  
C N | Cytochrome b | CYB_YEAST  
D O | Cytochrome c1, heme protein, mitochondrial | CY1_YEAST  
E P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_YEAST  
F Q | Cytochrome b-c1 complex subunit 6 | QCR6_YEAST  
G R | Cytochrome b-c1 complex subunit 7 | QCR7_YEAST  
H S | Cytochrome b-c1 complex subunit 8 | QCR8_YEAST  
I T | Cytochrome b-c1 complex subunit 9 | QCR9_YEAST  
J U | Cytochrome b-c1 complex subunit 10 | QCR10_YEAST  
a n | Cytochrome c oxidase subunit 1 | COX1_YEAST  
b o | Cytochrome c oxidase subunit 2 | COX2_YEAST  
c p | Cytochrome c oxidase subunit 3 | COX3_YEAST  
d q | Cytochrome c oxidase subunit 4, mitochondrial | COX4_YEAST  
e r | Cytochrome c oxidase polypeptide 5B, mitochondrial | COX5B_YEAST  
f s | Cytochrome c oxidase subunit 6, mitochondrial | COX6_YEAST  
g t | Cytochrome c oxidase subunit 7 | COX7_YEAST  
h u | Cytochrome c oxidase polypeptide VIII, mitochondrial | COX8_YEAST  
i v | Cytochrome c oxidase subunit 7A | COX9_YEAST  
j w | Cytochrome c oxidase subunit 6B | COX12_YEAST  
k x | Cytochrome c oxidase subunit 6A, mitochondrial | COX13_YEAST  
l y | Cox26 | YD19A_YEAST  
m z | Respiratory supercomplex factor 2, mitochondrial | RCF2_YEAST  
  
Non-standard residues in 6t0b #1  
---  
CA — calcium ion  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
CU — copper (II) ion  
CUA — dinuclear copper ion  
FES — FE2/S2 (inorganic) cluster  
HEA — heme-A  
HEC — heme C  
HEM — protoporphyrin IX containing Fe (HEME)  
MG — magnesium ion  
PCF — 1,2-diacyl-Sn-glycero-3-phoshocholine  
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)  
ZN — zinc ion  
  

> open 10340 fromDatabase emdb

Summary of feedback from opening 10340 fetched from emdb  
---  
note | Fetching compressed map 10340 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10340/map/emd_10340.map.gz  
  
Opened emdb 10340 as #2, grid size 448,448,448, pixel 1.09, shown at level
0.203, step 2, values float32  

> volume #2 color #b2ffb226

> volume #2 step 1

> volume gaussian #2 bfactor 150

Opened emdb 10340 gaussian as #3, grid size 448,448,448, pixel 1.09, shown at
step 1, values float32  

> volume #3 color #e5bf9923

> volume #3 color #e5bf9924

> molmap #1&protein 6

Opened 6t0b map 6 as #4, grid size 75,102,162, pixel 2, shown at level 0.101,
step 1, values float32  

> hide #!1 models

> select clear

> show #!1 models

> coulombic #1&protein

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/g ALA 60 OXT  
/e LYS 151 OXT  
/t ALA 60 OXT  
/c VAL 269 OXT  
/p VAL 269 OXT  
/r LYS 151 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS+TYR (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmptagh7mnv/ante.in.mol2 -fi
mol2 -o
/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmptagh7mnv/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(HIS+TYR) ``  
(HIS+TYR) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIS+TYR) ``  
(HIS+TYR) `Info: Finished reading file
(/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmptagh7mnv/ante.in.mol2);
atoms read (63), bonds read (64).`  
(HIS+TYR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIS+TYR) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIS+TYR) ``  
(HIS+TYR) ``  
(HIS+TYR) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIS+TYR) `Info: Total number of electrons: 244; net charge: 0`  
(HIS+TYR) ``  
(HIS+TYR) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(HIS+TYR) ``  
(HIS+TYR) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(HIS+TYR) ``  
(HIS+TYR) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIS+TYR) ``  
Charges for residue HIS+TYR determined  
Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69,
maximum 12.75  
Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57,
maximum 9.66  
Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34,
maximum 13.75  
Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12,
maximum 26.17  
Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41,
maximum 15.32  
Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07,
maximum 6.06  
Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98,
maximum 10.07  
Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67,
maximum 11.34  
Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56,
maximum 19.51  
Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48,
maximum 11.81  
Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78,
maximum 11.40  
Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65,
maximum 9.34  
Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27,
maximum 14.16  
Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18,
maximum 22.82  
Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67,
maximum 15.86  
Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18,
maximum 6.42  
Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01,
maximum 8.56  
Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72,
maximum 12.05  
Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52,
maximum 14.49  
Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50,
maximum 10.22  
Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12,
maximum 14.50  
Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63,
maximum 9.06  
Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32,
maximum 9.43  
Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79,
maximum 8.25  
Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35,
maximum 8.80  
Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54,
maximum 5.74  
Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54,
maximum 18.83  
Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85,
maximum 14.99  
Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40,
maximum 11.38  
Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70,
maximum 8.57  
Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49,
maximum 11.03  
Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32,
maximum 7.92  
Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70,
maximum 10.31  
Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07,
maximum 13.36  
Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61,
maximum 8.69  
Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65,
maximum 9.81  
Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80,
maximum 11.90  
Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40,
maximum 9.19  
Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52,
maximum 7.54  
Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58,
maximum 19.92  
Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68,
maximum 13.20  
Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57,
maximum 12.66  
Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91,
maximum 8.16  
Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44,
maximum 9.03  
Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32,
maximum 8.49  
Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62,
maximum 11.63  

> ~cartoon #1

> show #1&|protein

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1&~protein

> set bgColor white

> color #1:CDL,PEF green

> usage clip

clip [near near] [far far] [front front] [back back] [position center point]
[axis an axis vector] [coordinateSystem a coordinate-system]  
— set clip planes  
near: off or a number  
far: off or a number  
front: off or a number  
back: off or a number

clip list  
— List active clip planes

clip model models [clipping]  
— Turn off clipping for individual models.  
clipping: true or false

clip off  
— Turn off all clip planes  

> clip model #3 false

> camera ortho

> clip near offset 1

Invalid "near" argument: Expected 'off' or a number  

> clip near 1

[Repeated 7 time(s)]

> clip near 10

[Repeated 4 time(s)]

> clip near -50

> usage clip cap

clip [near near] [far far] [front front] [back back] [position center point]
[axis an axis vector] [coordinateSystem a coordinate-system]  
— set clip planes  
near: off or a number  
far: off or a number  
front: off or a number  
back: off or a number

clip list  
— List active clip planes

clip model models [clipping]  
— Turn off clipping for individual models.  
clipping: true or false

clip off  
— Turn off all clip planes  

> usage clip

clip [near near] [far far] [front front] [back back] [position center point]
[axis an axis vector] [coordinateSystem a coordinate-system]  
— set clip planes  
near: off or a number  
far: off or a number  
front: off or a number  
back: off or a number

clip list  
— List active clip planes

clip model models [clipping]  
— Turn off clipping for individual models.  
clipping: true or false

clip off  
— Turn off all clip planes  

> usage cap

"cap" is not a command name  

> usage surf

surface [atoms] [enclose an atoms specifier] [include an atoms specifier]
[probeRadius a number] [gridSpacing a number] [resolution a number] [level a
number] [color a color] [transparency a number] [visiblePatches an integer]
[sharpBoundaries true or false] [nthread an integer] [replace true or false]
[update true or false]  
— create molecular surface  
Subcommands are:

  * surface cap
  * surface check
  * surface close
  * surface dust
  * surface hidePatches
  * surface showall
  * surface showPatches
  * surface splitbycolor
  * surface squaremesh
  * surface style
  * surface undust
  * surface unzone
  * surface zone

  

> usage surf cap

surface cap [enable] [offset a number] [subdivision a number] [mesh true or
false]  
— Enable or disable clipping surface caps  
enable: true or false  

> surface color lightgrey

> coulombic #1&protein

Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69,
maximum 12.75  
Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57,
maximum 9.66  
Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34,
maximum 13.75  
Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12,
maximum 26.17  
Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41,
maximum 15.32  
Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07,
maximum 6.06  
Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98,
maximum 10.07  
Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67,
maximum 11.34  
Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56,
maximum 19.51  
Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48,
maximum 11.81  
Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78,
maximum 11.40  
Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65,
maximum 9.34  
Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27,
maximum 14.16  
Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18,
maximum 22.82  
Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67,
maximum 15.86  
Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18,
maximum 6.42  
Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01,
maximum 8.56  
Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72,
maximum 12.05  
Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52,
maximum 14.49  
Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50,
maximum 10.22  
Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12,
maximum 14.50  
Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63,
maximum 9.06  
Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32,
maximum 9.43  
Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79,
maximum 8.25  
Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35,
maximum 8.80  
Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54,
maximum 5.74  
Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54,
maximum 18.83  
Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85,
maximum 14.99  
Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40,
maximum 11.38  
Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70,
maximum 8.57  
Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49,
maximum 11.03  
Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32,
maximum 7.92  
Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70,
maximum 10.31  
Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07,
maximum 13.36  
Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61,
maximum 8.69  
Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65,
maximum 9.81  
Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80,
maximum 11.90  
Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40,
maximum 9.19  
Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52,
maximum 7.54  
Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58,
maximum 19.92  
Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68,
maximum 13.20  
Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57,
maximum 12.66  
Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91,
maximum 8.16  
Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44,
maximum 9.03  
Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32,
maximum 8.49  
Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62,
maximum 11.63  

> clip near 50

[Repeated 1 time(s)]

> clip near -50

[Repeated 1 time(s)]

> clip near 10

[Repeated 9 time(s)]

> clip near -20

> clip near -200

> surface color lightgrey

> coulombic #1&protein

Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69,
maximum 12.75  
Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57,
maximum 9.66  
Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34,
maximum 13.75  
Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12,
maximum 26.17  
Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41,
maximum 15.32  
Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07,
maximum 6.06  
Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98,
maximum 10.07  
Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67,
maximum 11.34  
Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56,
maximum 19.51  
Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48,
maximum 11.81  
Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78,
maximum 11.40  
Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65,
maximum 9.34  
Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27,
maximum 14.16  
Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18,
maximum 22.82  
Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67,
maximum 15.86  
Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18,
maximum 6.42  
Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01,
maximum 8.56  
Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72,
maximum 12.05  
Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52,
maximum 14.49  
Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50,
maximum 10.22  
Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12,
maximum 14.50  
Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63,
maximum 9.06  
Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32,
maximum 9.43  
Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79,
maximum 8.25  
Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35,
maximum 8.80  
Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54,
maximum 5.74  
Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54,
maximum 18.83  
Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85,
maximum 14.99  
Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40,
maximum 11.38  
Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70,
maximum 8.57  
Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49,
maximum 11.03  
Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32,
maximum 7.92  
Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70,
maximum 10.31  
Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07,
maximum 13.36  
Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61,
maximum 8.69  
Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65,
maximum 9.81  
Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80,
maximum 11.90  
Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40,
maximum 9.19  
Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52,
maximum 7.54  
Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58,
maximum 19.92  
Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68,
maximum 13.20  
Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57,
maximum 12.66  
Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91,
maximum 8.16  
Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44,
maximum 9.03  
Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32,
maximum 8.49  
Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62,
maximum 11.63  

> clip near 20

[Repeated 7 time(s)]

> clip near -100

> close #1.28#1.2-27,29-47

> coulombic #1&protein

Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69,
maximum 12.75  
Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57,
maximum 9.66  
Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34,
maximum 13.75  
Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12,
maximum 26.17  
Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41,
maximum 15.32  
Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07,
maximum 6.06  
Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98,
maximum 10.07  
Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67,
maximum 11.34  
Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56,
maximum 19.51  
Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48,
maximum 11.81  
Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78,
maximum 11.40  
Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65,
maximum 9.34  
Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27,
maximum 14.16  
Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18,
maximum 22.82  
Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67,
maximum 15.86  
Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18,
maximum 6.42  
Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01,
maximum 8.56  
Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72,
maximum 12.05  
Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52,
maximum 14.49  
Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50,
maximum 10.22  
Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12,
maximum 14.50  
Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63,
maximum 9.06  
Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32,
maximum 9.43  
Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79,
maximum 8.25  
Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35,
maximum 8.80  
Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54,
maximum 5.74  
Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54,
maximum 18.83  
Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85,
maximum 14.99  
Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40,
maximum 11.38  
Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70,
maximum 8.57  
Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49,
maximum 11.03  
Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32,
maximum 7.92  
Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70,
maximum 10.31  
Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07,
maximum 13.36  
Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61,
maximum 8.69  
Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65,
maximum 9.81  
Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80,
maximum 11.90  
Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40,
maximum 9.19  
Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52,
maximum 7.54  
Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58,
maximum 19.92  
Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68,
maximum 13.20  
Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57,
maximum 12.66  
Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91,
maximum 8.16  
Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44,
maximum 9.03  
Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32,
maximum 8.49  
Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62,
maximum 11.63  

> surface color lightgrey

> coulombic #1&protein

Coulombic values for 6t0b_A SES surface #1.2: minimum, -17.95, mean -1.69,
maximum 12.75  
Coulombic values for 6t0b_B SES surface #1.3: minimum, -16.91, mean -1.57,
maximum 9.66  
Coulombic values for 6t0b_C SES surface #1.4: minimum, -11.90, mean 0.34,
maximum 13.75  
Coulombic values for 6t0b_D SES surface #1.5: minimum, -22.30, mean -2.12,
maximum 26.17  
Coulombic values for 6t0b_E SES surface #1.6: minimum, -17.51, mean -1.41,
maximum 15.32  
Coulombic values for 6t0b_F SES surface #1.7: minimum, -20.59, mean -5.07,
maximum 6.06  
Coulombic values for 6t0b_G SES surface #1.8: minimum, -14.12, mean -1.98,
maximum 10.07  
Coulombic values for 6t0b_H SES surface #1.9: minimum, -12.07, mean 0.67,
maximum 11.34  
Coulombic values for 6t0b_I SES surface #1.10: minimum, -9.78, mean 1.56,
maximum 19.51  
Coulombic values for 6t0b_J SES surface #1.11: minimum, -16.07, mean -0.48,
maximum 11.81  
Coulombic values for 6t0b_L SES surface #1.12: minimum, -17.13, mean -1.78,
maximum 11.40  
Coulombic values for 6t0b_M SES surface #1.13: minimum, -17.13, mean -1.65,
maximum 9.34  
Coulombic values for 6t0b_N SES surface #1.14: minimum, -10.79, mean 0.27,
maximum 14.16  
Coulombic values for 6t0b_O SES surface #1.15: minimum, -22.49, mean -2.18,
maximum 22.82  
Coulombic values for 6t0b_P SES surface #1.16: minimum, -15.87, mean -1.67,
maximum 15.86  
Coulombic values for 6t0b_Q SES surface #1.17: minimum, -19.39, mean -5.18,
maximum 6.42  
Coulombic values for 6t0b_R SES surface #1.18: minimum, -14.93, mean -2.01,
maximum 8.56  
Coulombic values for 6t0b_S SES surface #1.19: minimum, -12.58, mean 0.72,
maximum 12.05  
Coulombic values for 6t0b_T SES surface #1.20: minimum, -9.80, mean 1.52,
maximum 14.49  
Coulombic values for 6t0b_U SES surface #1.21: minimum, -14.13, mean -0.50,
maximum 10.22  
Coulombic values for 6t0b_a SES surface #1.22: minimum, -20.86, mean -1.12,
maximum 14.50  
Coulombic values for 6t0b_b SES surface #1.23: minimum, -22.89, mean -4.63,
maximum 9.06  
Coulombic values for 6t0b_c SES surface #1.24: minimum, -17.19, mean -1.32,
maximum 9.43  
Coulombic values for 6t0b_d SES surface #1.25: minimum, -18.56, mean -2.79,
maximum 8.25  
Coulombic values for 6t0b_e SES surface #1.26: minimum, -12.86, mean -0.35,
maximum 8.80  
Coulombic values for 6t0b_f SES surface #1.27: minimum, -16.70, mean -4.54,
maximum 5.74  
Coulombic values for 6t0b_g SES surface #1.28: minimum, -6.64, mean 3.54,
maximum 18.83  
Coulombic values for 6t0b_h SES surface #1.29: minimum, -8.95, mean 1.85,
maximum 14.99  
Coulombic values for 6t0b_i SES surface #1.30: minimum, -16.63, mean 1.40,
maximum 11.38  
Coulombic values for 6t0b_j SES surface #1.31: minimum, -11.24, mean -0.70,
maximum 8.57  
Coulombic values for 6t0b_k SES surface #1.32: minimum, -12.01, mean -0.49,
maximum 11.03  
Coulombic values for 6t0b_l SES surface #1.33: minimum, -8.58, mean 0.32,
maximum 7.92  
Coulombic values for 6t0b_m SES surface #1.34: minimum, -13.83, mean 0.70,
maximum 10.31  
Coulombic values for 6t0b_n SES surface #1.35: minimum, -27.12, mean -1.07,
maximum 13.36  
Coulombic values for 6t0b_o SES surface #1.36: minimum, -22.59, mean -4.61,
maximum 8.69  
Coulombic values for 6t0b_p SES surface #1.37: minimum, -17.24, mean -1.65,
maximum 9.81  
Coulombic values for 6t0b_q SES surface #1.38: minimum, -18.63, mean -2.80,
maximum 11.90  
Coulombic values for 6t0b_r SES surface #1.39: minimum, -16.19, mean -0.40,
maximum 9.19  
Coulombic values for 6t0b_s SES surface #1.40: minimum, -17.28, mean -4.52,
maximum 7.54  
Coulombic values for 6t0b_t SES surface #1.41: minimum, -7.43, mean 3.58,
maximum 19.92  
Coulombic values for 6t0b_u SES surface #1.42: minimum, -11.10, mean 1.68,
maximum 13.20  
Coulombic values for 6t0b_v SES surface #1.43: minimum, -15.96, mean 1.57,
maximum 12.66  
Coulombic values for 6t0b_w SES surface #1.44: minimum, -18.91, mean -0.91,
maximum 8.16  
Coulombic values for 6t0b_x SES surface #1.45: minimum, -13.37, mean -0.44,
maximum 9.03  
Coulombic values for 6t0b_y SES surface #1.46: minimum, -9.33, mean 0.32,
maximum 8.49  
Coulombic values for 6t0b_z SES surface #1.47: minimum, -20.56, mean 0.62,
maximum 11.63  

> clip near 20

[Repeated 8 time(s)]

> clip #3 false

Expected a keyword  

> usage clip

clip [near near] [far far] [front front] [back back] [position center point]
[axis an axis vector] [coordinateSystem a coordinate-system]  
— set clip planes  
near: off or a number  
far: off or a number  
front: off or a number  
back: off or a number

clip list  
— List active clip planes

clip model models [clipping]  
— Turn off clipping for individual models.  
clipping: true or false

clip off  
— Turn off all clip planes  

> clip model #3 false

> color #3 #3febe324 models

[Repeated 2 time(s)]

> select :CDL,PEF

1455 atoms, 1421 bonds, 34 residues, 1 model selected  

> style sel sphere

Changed 1455 atom styles  

> select clear

> movie record

> usage perframe

perframe command [ranges ranges] [frames an integer] [interval an integer]
[format a text string] [zeroPadWidth an integer] [showCommands true or false]  
— Run a command before each graphics frame is drawn  
command: a text string  
ranges: a range, repeatable

perframe stop  
— Stop all perframe commands  

> perframe "clip near 1" frames 250

> movie stop

> movie encode /Users/tcroll/Desktop/6t0b_tunnels.mp4

Movie saved to /Users/tcroll/Desktop/6t0b_tunnels.mp4  
  

> clip near -250

> movie record

> movie stop

> usage movie record

movie record [directory name of a folder to save/write; a name of 'browse'
will bring up a file browser] [pattern a text string] [format format] [size
size] [supersample an integer] [limit an integer]  
— Start saving frames of a movie to image files  
format: one of JPEG, PNG, or PPM  
size: some integers  

> windowsize

window size 1344 761  

> movie record

> perframe "clip near 0.25" frames 800

> movie stop

> pwd

Current working directory is: /Users/tcroll/Desktop  

> movie encode 6t0b_flythrough.mp4

Movie saved to 6t0b_flythrough.mp4  
  

> close #2-4#1.2-47

> close

> isolde demo crystal_intro

> set selectionWidth 4

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description | UniProt  
A | predicted microcompartment protein | A5N734_CLOK5  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description | UniProt  
1.2/A | predicted microcompartment protein | A5N734_CLOK5  
  

WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,34,34, pixel 0.723, shown at
level 0.0949, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,34,34, pixel 0.723, shown at
level -0.057,0.057, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,34,34, pixel 0.723,
shown at level 0.346, step 1, values float32  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 12 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,34,34, pixel 0.723,
shown at level 0.305, step 1, values float32  
Loaded crystallographic demo: PDB ID 3io0  

Populating font family aliases took 214 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

> IEP

Unknown command: alphafold IEP  

> isolde add ligand IEP

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

> close #1.1

Deleting Crystallographic maps(3io0-sf.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) MDFF potential  

> delete ~:IEP

> delete sel

[Repeated 3 time(s)]

> save /Users/tcroll/Desktop/IEP.pdb #1

> isolde parameterise sel

Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmpx57qchd1/ante.in.mol2 -fi
mol2 -o
/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmpx57qchd1/ante.out.mol2 -fo
mol2 -c bcc -nc -5 -j 5 -s 2 -dr n  
(IEP) ``  
(IEP) `Welcome to antechamber 20.0: molecular input file processor.`  
(IEP) ``  
(IEP) `Info: Finished reading file
(/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmpx57qchd1/ante.in.mol2);
atoms read (149), bonds read (149).`  
(IEP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(IEP) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(IEP) ``  
(IEP) ``  
(IEP) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(IEP) `Info: Total number of electrons: 564; net charge: -5`  
(IEP) ``  
(IEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(IEP) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(IEP) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Failure running ANTECHAMBER for residue IEP Check reply log for details  

> save iep.mol2 #1

> show

> usage bondrot

"bondrot" is not a command name  

> usage rotate

"rotate" is not a command name  

> ui mousemode right "bond rotation"

> torsion /A:1000@C59,C58,C57,C56 -84.06

> torsion /A:1000@C59,C58,C57,C56 21.72

> torsion /A:1000@C62,C61,C60,C59 -70.26

> torsion /A:1000@C62,C61,C60,C59 -14.03

> torsion /A:1000@C59,C58,C57,C56 6.39

> torsion /A:1000@C30,C29,O28,P25 -52.61

> torsion /A:1000@C30,C29,O28,P25 -64.56

> torsion /A:1000@H74,O47,C30,C29 -61.19

> torsion /A:1000@C29,O28,P25,O24 157.50

> torsion /A:1000@P37,O36,C33,C32 122.89

> save iep.mol2 #1

> torsion /A:1000@C30,C29,O28,P25 -155.19

> torsion /A:1000@C15,C16,C17,C18 102.52

> torsion /A:1000@C60,C59,C58,C57 160.98

> torsion /A:1000@C58,C57,C56,C55 134.76

> torsion /A:1000@C63,C62,C61,C60 102.67

> torsion /A:1000@C56,C55,C54,C53 1.93

> torsion /A:1000@C57,C56,C55,C54 141.08

> save iep.mol2 #1

> coulombic #1

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue IEP (net charge -5) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.in.mol2 -fi
mol2 -o
/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.out.mol2 -fo
mol2 -c bcc -nc -5 -j 5 -s 2 -dr n  
(IEP) ``  
(IEP) `Welcome to antechamber 20.0: molecular input file processor.`  
(IEP) ``  
(IEP) `Info: Finished reading file
(/var/folders/ps/9wr_2p092f7_c6szng_0gcy80000gr/T/tmp2r7n3nw2/ante.in.mol2);
atoms read (149), bonds read (149).`  
(IEP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(IEP) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(IEP) ``  
(IEP) ``  
(IEP) `Running:
/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(IEP) `Info: Total number of electrons: 564; net charge: -5`  
(IEP) ``  
(IEP) `Running: /Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(IEP) `/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(IEP) `Cannot properly run
"/Applications/ChimeraX-1.4.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Failure running ANTECHAMBER for residue IEP Check reply log for details  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 37 days 3:06

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0.dev0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (6)

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 → Report sqm.out; try to make quotes "reusable"

comment:2 by Eric Pettersen, 3 years ago

Just FYI, with all those phosphates in IEP the sqm failure is probably a failure to converge.

in reply to:  3 ; comment:3 by Tristan Croll, 3 years ago 

Got it in one! So far I’ve managed to get it to last a *little* longer by
tweaking the starting geometry to keep the phosphates further apart, but no
luck getting a stable run so far. Any hints?

On Mon, 26 Sep 2022 at 19:16, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:4 by Eric Pettersen, 3 years ago

If I isolate IEP from chain A of 5zm8, coulombic works on it after about 20-30 minutes of cogitating in the Sept. 21 daily build on my Mac. The net charge is -3 instead of -5, because addh adds protons to the two terminal phosphates. Protons get added to such phosphates based on the O-P bond lengths -- one has to be at least 0.05A longer than the other two. You could "force" this by assigning O3 as the IDATM type of an oxygen on each.

in reply to:  5 ; comment:5 by Tristan Croll, 3 years ago 

Yeah, I was starting from the “ideal” (ha!) coordinates from the components
dictionary, with -5 net charge. Will have to take a close look at the
target site to consider what protonation state makes most sense. Thanks for
the tip!

On Mon, 26 Sep 2022 at 19:52, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:6 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: accepted → closed

The contents of sqm.out are now also dumped on an antechamber failure (daily build only). I could not replicate your problem with the weird quotes. When I copy from the log and paste as input to 'od -x', they are normal single-quote characters (hex 27). Maybe whatever you pasted into transformed the quotes?

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