All residues in MAE file erroneously non-standard

[phil.cruz@…]

The following bug report has been submitted:
Platform:        macOS-12.6-arm64-arm-64bit
ChimeraX Version: 1.5.dev202210022132 (2022-10-02 21:32:10 UTC)
Description
Applying the NIH 3D preset for surface coulombic with the attached file gives the error.  Note that the preset for surface hydrophobicity doesn't give an error, but also makes the whole surface magenta.
Although this was reported on an M1 Mac, it happens on other computers too.

Log:
UCSF ChimeraX version: 1.5.dev202210022132 (2022-10-02)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/cruzp2/Downloads/glide-dock_lps_xp_mod4_6.mae format
> "schrodinger maestro"

Chain information for glide-dock_lps_xp_mod4_6.mae  
---  
Chain | Description  
1.1/A | No description available  
  
Opened glide-dock_lps_xp_mod4_6.mae containing 2 structures (5518 atoms, 5584
bonds)  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 5518 atom radii, 5584 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
1777 atoms, 1451 bonds, 354 residues, 1 model selected  
Nothing selected  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    delete H
    preset 'initial styles' cartoon
    nucleotides ladder radius 1.2
    color white target abc
    color helix marine
    color strand firebrick
    color coil goldenrod
    color nucleic-acid forest
    color :A:C:G:U grape
    color byatom
    select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide)
    color sel carbon_grey atoms
    color ligand | protein & sideonly byhet atoms
    ~select
    rainbow #1.1@ca,c4' chains palette marine:marine target rs
    rainbow #1.2.1@ca,c4' chains palette marine:marine target rs

  

> preset nih3d "ribbon by chain (printable)"

Using preset: NIH3D / Ribbon by Chain (Printable)  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
1777 atoms, 1451 bonds, 354 residues, 1 model selected  
Nothing selected  
Changed 0 pseudobond radii  
Changed 0 atom radii  
1416 atoms, 1415 bonds, 354 residues, 1 model selected  
192 hydrogen bonds found  
Changed 192 pseudobond radii  
Created 53 struts for @ca | ligand | P | ##num_atoms<500, max length 8, max
loop length 60  
  
Nothing selected  
Changed 2870 bond radii  
Changed 2 pseudobond dashes  
Preset expands to these ChimeraX commands:

    
    
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    delete H
    preset 'initial styles' cartoon
    nucleotides ladder radius 1.2
    color white target abc
    color helix marine
    color strand firebrick
    color coil goldenrod
    color nucleic-acid forest
    color :A:C:G:U grape
    color byatom
    select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide)
    color sel carbon_grey atoms
    color ligand | protein & sideonly byhet atoms
    ~select
    rainbow #1.1@ca,c4' chains palette marine:marine target rs
    rainbow #1.2.1@ca,c4' chains palette marine:marine target rs
    size min-backbone pseudobondRadius 1.1
    size ions atomRadius +0.8
    select backbone & protein | nucleic-acid & min-backbone | ions | ligand | ligand :< 5 & ~nucleic-acid
    hbonds sel color white restrict both
    size pseudobondRadius 0.6
    wait 1
    struts @ca|ligand|P|##num_atoms<500 length 8 loop 60 rad 0.75 color struts_grey
    ~struts @PB,PG resetRibbon false
    ~struts adenine|cytosine|guanine|thymine|uracil resetRibbon false
    color hbonds white pseudobonds
    ~select
    size stickRadius 0.8
    style dashes 0

  

> preset nih3d "ribbon by secondary structure"

Using preset: NIH3D / Ribbon by Secondary Structure  
Changed 2804 atom radii, 2870 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
1777 atoms, 1451 bonds, 354 residues, 1 model selected  
Nothing selected  
Preset expands to these ChimeraX commands:

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

  

> preset nih3d "ribbon rainbow"

Using preset: NIH3D / Ribbon Rainbow  
Changed 2804 atom radii, 2870 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
1777 atoms, 1451 bonds, 354 residues, 1 model selected  
Nothing selected  
Preset expands to these ChimeraX commands:

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

  

> preset nih3d "surface by chain"

Using preset: NIH3D / Surface by Chain  
Changed 2804 atom radii, 2870 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 glide-dock_lps_xp_mod4_6.mae #1.1  
---  
notes | No usable SEQRES records for glide-dock_lps_xp_mod4_6.mae (#1.1) chain
A; guessing termini instead  
Chain-initial residues that are actual N termini: glide-dock_lps_xp_mod4_6.mae
#1.1/A MET 1  
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: glide-
dock_lps_xp_mod4_6.mae #1.1/A VAL 354  
340 hydrogen bonds  
glide-dock_lps_xp_mod4_6.mae #1.1/A VAL 354 is not terminus, removing H atom
from 'C'  
2677 hydrogens added  
  
Summary of feedback from adding hydrogens to glide-dock_lps_xp_mod4_6.mae
#1.2.1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
6 hydrogen bonds  
33 hydrogens added  
  
Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    addh #1.2.1
    surface #1.1 enclose #1.1 grid 0.941538 sharp true
    surface #1.2.1 enclose #1.2.1 grid 0.5 sharp true
    rainbow #1.1@ca,c4' chains palette marine:marine target rsa
    color zone #1.1 near #1.1 distance 20
    rainbow #1.2.1@ca,c4' chains palette marine:marine target rsa
    color zone #1.2.1 near #1.2.1 distance 20

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 5514 atom radii, 5580 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to glide-dock_lps_xp_mod4_6.mae #1.1  
---  
notes | No usable SEQRES records for glide-dock_lps_xp_mod4_6.mae (#1.1) chain
A; guessing termini instead  
Chain-initial residues that are actual N termini: glide-dock_lps_xp_mod4_6.mae
#1.1/A MET 1  
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: glide-
dock_lps_xp_mod4_6.mae #1.1/A VAL 354  
315 hydrogen bonds  
glide-dock_lps_xp_mod4_6.mae #1.1/A VAL 354 is not terminus, removing H atom
from 'C'  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to glide-dock_lps_xp_mod4_6.mae
#1.2.1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
3 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1171, in <lambda>  
run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower()))))  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/preset_mgr/cmd.py", line 50, in preset_cmd  
run_preset(session, cat, matches[0])  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/preset_mgr/cmd.py", line 71, in run_preset  
session.presets.preset_function(category, preset)()  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/preset_mgr/manager.py", line 60, in cb  
bi.run_provider(self.session, name, self)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/cruzp2/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/nih_presets/__init__.py", line 22, in run_provider  
run_preset(session, name, mgr, **kw)  
File "/Users/cruzp2/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/nih_presets/presets.py", line 286, in run_preset  
mgr.execute(cmd)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/preset_mgr/manager.py", line 88, in execute  
run(self.session, line, log=False)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 178, in add_standard_charges  
fr = FakeRes(connected)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 727, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
ValueError: Could not come up with unique atom name in mega-residue  
  
ValueError: Could not come up with unique atom name in mega-residue  
  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 727, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
  
See log for complete Python traceback.  
  

> preset nih3d "surface hydrophobicity"

Using preset: NIH3D / Surface Hydrophobicity  
Changed 5514 atom radii, 5580 bond radii, 0 pseudobond radii  
Changed 0 pseudobond dashes  
Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

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

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

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

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

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

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

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

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

  
Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
Summary of feedback from adding hydrogens to glide-dock_lps_xp_mod4_6.mae #1.1  
---  
notes | No usable SEQRES records for glide-dock_lps_xp_mod4_6.mae (#1.1) chain
A; guessing termini instead  
Chain-initial residues that are actual N termini: glide-dock_lps_xp_mod4_6.mae
#1.1/A MET 1  
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: glide-
dock_lps_xp_mod4_6.mae #1.1/A VAL 354  
315 hydrogen bonds  
glide-dock_lps_xp_mod4_6.mae #1.1/A VAL 354 is not terminus, removing H atom
from 'C'  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to glide-dock_lps_xp_mod4_6.mae
#1.2.1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
3 hydrogen bonds  
0 hydrogens added  
  

All 'kd_hydrophobicity' values are None  

Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    addh #1.2.1
    surface #1.1 enclose #1.1 grid 1.23568 sharp true
    surface #1.2.1 enclose #1.2.1 grid 0.5 sharp true
    color magenta
    color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta

  

> close session

> open /Users/cruzp2/Downloads/glide-dock_lps_xp_mod4_6.mae format
> "schrodinger maestro"

Chain information for glide-dock_lps_xp_mod4_6.mae  
---  
Chain | Description  
1.1/A | No description available  
  
Opened glide-dock_lps_xp_mod4_6.mae containing 2 structures (5518 atoms, 5584
bonds)  

> preset nih3d "surface hydrophobicity"

Using preset: NIH3D / Surface Hydrophobicity  
Changed 5518 atom radii, 5584 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 glide-dock_lps_xp_mod4_6.mae #1.1  
---  
notes | No usable SEQRES records for glide-dock_lps_xp_mod4_6.mae (#1.1) chain
A; guessing termini instead  
Chain-initial residues that are actual N termini: glide-dock_lps_xp_mod4_6.mae
#1.1/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: glide-dock_lps_xp_mod4_6.mae
#1.1/A VAL 354  
Chain-final residues that are not actual C termini:  
326 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to glide-dock_lps_xp_mod4_6.mae
#1.2.1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
0 hydrogens added  
  

All 'kd_hydrophobicity' values are None  

Preset expands to these ChimeraX commands:

    
    
    ~struts
    ~hbonds
    size atomRadius default stickRadius 0.2 pseudobondRadius 0.2
    style dashes 7
    graphics bgcolor white
    color name marine 0,50,100
    color name forest 13.3,54.5,13.3
    color name tangerine 95.3,51.8,0
    color name grape 64.3,0,86.7
    color name nih_blue 12.5,33.3,54.1
    color name jmol_carbon 56.5,56.5,56.5
    color name bond_purple 57.6,43.9,85.9
    color name struts_grey 48,48,48
    color name carbon_grey 22.2,22.2,22.2
    surface close
    preset 'initial styles' 'original look'
    delete solvent
    hide H|ligand|~(protein|nucleic-acid)
    ~nuc
    ~ribbon
    ~display
    addh #1.1
    addh #1.2.1
    surface #1.1 enclose #1.1 grid 1.236 sharp true
    surface #1.2.1 enclose #1.2.1 grid 0.5 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 5518 atom radii, 5584 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 glide-dock_lps_xp_mod4_6.mae #1.1  
---  
notes | No usable SEQRES records for glide-dock_lps_xp_mod4_6.mae (#1.1) chain
A; guessing termini instead  
Chain-initial residues that are actual N termini: glide-dock_lps_xp_mod4_6.mae
#1.1/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: glide-dock_lps_xp_mod4_6.mae
#1.1/A VAL 354  
Chain-final residues that are not actual C termini:  
326 hydrogen bonds  
0 hydrogens added  
  
Summary of feedback from adding hydrogens to glide-dock_lps_xp_mod4_6.mae
#1.2.1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
4 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1171, in <lambda>  
run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower()))))  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/preset_mgr/cmd.py", line 50, in preset_cmd  
run_preset(session, cat, matches[0])  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/preset_mgr/cmd.py", line 71, in run_preset  
session.presets.preset_function(category, preset)()  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/preset_mgr/manager.py", line 60, in cb  
bi.run_provider(self.session, name, self)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/cruzp2/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/nih_presets/__init__.py", line 22, in run_provider  
run_preset(session, name, mgr, **kw)  
File "/Users/cruzp2/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/nih_presets/presets.py", line 286, in run_preset  
mgr.execute(cmd)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/preset_mgr/manager.py", line 88, in execute  
run(self.session, line, log=False)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 178, in add_standard_charges  
fr = FakeRes(connected)  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 727, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
ValueError: Could not come up with unique atom name in mega-residue  
  
ValueError: Could not come up with unique atom name in mega-residue  
  
File
"/Users/cruzp2/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 727, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
  
See log for complete Python traceback.  
  




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

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 2:42

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Thunderbolt Display:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        BenQ GW2750H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.3
    ChimeraX-AtomicLibrary: 8.0.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.2
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202210022132
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.0.6
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.0
    filelock: 3.7.1
    fonttools: 4.37.4
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.4
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File attachment: glide-dock_lps_xp_mod4_6.mae

glide-dock_lps_xp_mod4_6.mae​

[phil.cruz@…]

Added by email2trac

[Eric Pettersen]

Hi Phil,

If you look in the Select→Residues menu you can see that ChimeraX thinks all the residues are non-standard (when they clearly aren't). I will have to investigate.

--Eric

[Eric Pettersen]

Fixed. Maestro reader was including a trailing space in residue names. Fix in tomorrow's daily build.