mlp surfaces option uses wrong atoms

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.6-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202210132007 (2022-10-13 20:07:18 UTC)
Description
The mlp command surfaces argument uses the surface associated atoms even if those are not contained in the atoms specified as the first argument to the mlp command.

That gives "Inf" values in this case where I was trying to color a channel surface made on atom markers produced by moleonline.

I think if the surface associated atoms are not in the mlp specified atoms then the mlp specified atoms should be used.


Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.5.dev202210050037 (2022-10-13)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3lbw

Summary of feedback from opening 3lbw fetched from pdb  
---  
notes | Fetching compressed mmCIF 3lbw from
http://files.rcsb.org/download/3lbw.cif  
Fetching CCD Z82 from http://ligand-expo.rcsb.org/reports/Z/Z82/Z82.cif  
Fetching CCD XYL from http://ligand-expo.rcsb.org/reports/X/XYL/XYL.cif  
  
3lbw title:  
High resolution crystal structure of transmembrane domain of M2 [more info...]  
  
Chain information for 3lbw #1  
---  
Chain | Description | UniProt  
A B C D | M2 protein | Q9YP62_9INFA  
  
Non-standard residues in 3lbw #1  
---  
NH2 — amino group  
PEG — di(hydroxyethyl)ether  
XYL — Xylitol (D-Xylitol)  
Z82 — 4-bromobenzoic acid  
  

> open /Users/goddard/Downloads/mole_channels_iTVKHERsUakafWAMleTg_1.json

Opened 2 Mole channels in PDB 3lbw  

> surface #2.1

> hide #!2.1 models

> show #!2.1 models

> hide #2.1

> show #2.2 models

> surface #2.1

> surface #2.2

> hide #2

> help mlp

> mlp #1 surfaces #2

Map values for surface "Tunnel 1_A SES surface": minimum inf, mean inf,
maximum inf  
Map values for surface "Tunnel 2_A SES surface": minimum inf, mean inf,
maximum inf  

> surface #1

> mlp #1

Map values for surface "3lbw_A SES surface": minimum -20.52, mean 2.914,
maximum 20.97  
Map values for surface "3lbw_B SES surface": minimum -20.47, mean 3.126,
maximum 22.24  
Map values for surface "3lbw_C SES surface": minimum -21.65, mean 2.948,
maximum 21.36  
Map values for surface "3lbw_D SES surface": minimum -21.35, mean 2.93,
maximum 22.05  

> surface close #1

> mlp #1 surfaces #2.1

Map values for surface "Tunnel 1_A SES surface": minimum inf, mean inf,
maximum inf  

> help coulomb

> coulombic #1 surfaces #2

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue PEG (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp8ydzfkse/ante.in.mol2 -fi
mol2 -o
/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp8ydzfkse/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(PEG) ``  
(PEG) `Welcome to antechamber 20.0: molecular input file processor.`  
(PEG) ``  
(PEG) `Info: Finished reading file
(/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp8ydzfkse/ante.in.mol2);
atoms read (17), bonds read (16).`  
(PEG) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(PEG) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(PEG) ``  
(PEG) ``  
(PEG) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(PEG) `Info: Total number of electrons: 58; net charge: 0`  
(PEG) ``  
(PEG) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(PEG) ``  
(PEG) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(PEG) ``  
(PEG) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(PEG) ``  
Charges for residue PEG determined  
Assigning partial charges to residue XYL (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp1ddwq29u/ante.in.mol2 -fi
mol2 -o
/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp1ddwq29u/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(XYL) ``  
(XYL) `Welcome to antechamber 20.0: molecular input file processor.`  
(XYL) ``  
(XYL) `Info: Finished reading file
(/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp1ddwq29u/ante.in.mol2);
atoms read (22), bonds read (21).`  
(XYL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(XYL) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(XYL) ``  
(XYL) ``  
(XYL) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(XYL) `Info: Total number of electrons: 82; net charge: 0`  
(XYL) ``  
(XYL) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(XYL) ``  
(XYL) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(XYL) ``  
(XYL) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(XYL) ``  
Charges for residue XYL determined  
Assigning partial charges to residue Z82+PRO (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp10cewnvj/ante.in.mol2 -fi
mol2 -o
/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp10cewnvj/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(Z82+PRO) ``  
(Z82+PRO) `Welcome to antechamber 20.0: molecular input file processor.`  
(Z82+PRO) ``  
(Z82+PRO) `Info: Finished reading file
(/var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmp10cewnvj/ante.in.mol2);
atoms read (33), bonds read (34).`  
(Z82+PRO) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(Z82+PRO) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(Z82+PRO) ``  
(Z82+PRO) ``  
(Z82+PRO) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(Z82+PRO) `Info: Total number of electrons: 158; net charge: 0`  
(Z82+PRO) ``  
(Z82+PRO) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(Z82+PRO) ``  
(Z82+PRO) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(Z82+PRO) ``  
(Z82+PRO) `Running:
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(Z82+PRO) ``  
Charges for residue Z82+PRO determined  
Coulombic values for Tunnel 1_A SES surface #2.1.1: minimum, -1559.62, mean
18.13, maximum 1381.92  
Coulombic values for Tunnel 2_A SES surface #2.2.1: minimum, -7613.50, mean
-9.34, maximum 619.83  

> hide #1

> show #2 :<3

> show #2 :<5

> hide #2

> show #2 :<8

> hide #1

> show #2 :<6

> hide #2

> coulombic protein surfaces #2

Coulombic values for Tunnel 1_A SES surface #2.1.1: minimum, -1559.60, mean
18.14, maximum 1381.94  
Coulombic values for Tunnel 2_A SES surface #2.2.1: minimum, -7613.12, mean
-9.07, maximum 619.85  

> lighting soft

> lighting full

> lighting soft

> lighting multiShadow 256

> set bgColor white

> lighting multiShadow 512

> graphics silhouettes true

> windowsize 500 500

> save /Users/goddard/Desktop/image1.png supersample 3

> mlp #1 surfaces #2.1

Map values for surface "Tunnel 1_A SES surface": minimum inf, mean inf,
maximum inf  

> mlp #1 surfaces #2.1 map true

Opened mlp Tunnel as #3, grid size 23,32,22, pixel 1, shown at step 1, values
float32  
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/arrays.py:155: RuntimeWarning: invalid value
encountered in multiply  
v = fbc + b * bsize # Center of bin where rank crossed.  
Map values for surface "Tunnel 1_A SES surface": minimum inf, mean inf,
maximum inf  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2728, in update_cb  
s.update_histogram(rm, m, rz, delay = 0)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 2750, in update_histogram  
counts = s.bin_counts(bins)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/arrays.py", line 121, in bin_counts  
b0 = int(ceil(fb0))  
ValueError: cannot convert float NaN to integer  
  
ValueError: cannot convert float NaN to integer  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/arrays.py", line 121, in bin_counts  
b0 = int(ceil(fb0))  
  
See log for complete Python traceback.  
  

> mlp #1 map true

Opened mlp 3lbw_A as #4, grid size 34,55,39, pixel 1, shown at step 1, values
float32  
Map values for surface "3lbw_A SES surface": minimum -20.52, mean 2.914,
maximum 20.97  
Opened mlp 3lbw_B as #5, grid size 39,55,35, pixel 1, shown at step 1, values
float32  
Map values for surface "3lbw_B SES surface": minimum -20.47, mean 3.126,
maximum 22.24  
Opened mlp 3lbw_C as #6, grid size 35,52,43, pixel 1, shown at step 1, values
float32  
Map values for surface "3lbw_C SES surface": minimum -21.65, mean 2.948,
maximum 21.36  
Opened mlp 3lbw_D as #7, grid size 43,52,34, pixel 1, shown at step 1, values
float32  
Map values for surface "3lbw_D SES surface": minimum -21.35, mean 2.93,
maximum 22.05  

> close #3

> hide #!5 models

> hide #!6 models

> hide #!7 models

> surface #1 hide

Expected a keyword  

> surface close #1

> close #4-7

> mlp #1 map true color false

Opened mlp map as #3, grid size 47,56,47, pixel 1, shown at step 1, values
float32  

> mlp #1 color false surfaces #2

> ui tool show "Surface Color"

> color sample #2.1.1 map #3 palette #ff0000:#ffffff:#0000ff

Map values for surface "Tunnel 1_A SES surface": minimum -14.57, mean 5.157,
maximum 17.72  

> color sample #2 map #3 palette lipophilicity range -20,20

Map values for surface "Tunnel 1_A SES surface": minimum -14.57, mean 5.157,
maximum 17.72  
Map values for surface "Tunnel 2_A SES surface": minimum -16.49, mean -0.9156,
maximum 15.48  

> color sample #2 map #3 palette lipophilicity range -10,10

Map values for surface "Tunnel 1_A SES surface": minimum -14.57, mean 5.157,
maximum 17.72  
Map values for surface "Tunnel 2_A SES surface": minimum -16.49, mean -0.9156,
maximum 15.48  

> set bgColor black

> set bgColor transparent

> save /Users/goddard/Desktop/image1.png supersample 3

> surface close #2

> surface #2 resolution 3

2 Gaussian surfaces, threshold level 1.503 - 1.593  

> surface close #2

> surface enclose #2 sharpBoundaries false

> mlp #1 surfaces #2

Map values for surface "3lbw_A SES surface": minimum -20.52, mean 2.914,
maximum 20.97  
Map values for surface "3lbw_B SES surface": minimum -20.47, mean 3.126,
maximum 22.24  
Map values for surface "3lbw_C SES surface": minimum -21.65, mean 2.948,
maximum 21.36  
Map values for surface "3lbw_D SES surface": minimum -21.35, mean 2.93,
maximum 22.05  

> surface close #1

> hide #2.1 models

> hide #2.2 models

> mlp #1 surfaces #4

Map values for surface "Surface #2": minimum 286.5, mean 720.1, maximum 1624  

> close #4

> show #2.1 models

> show #2.2 models

> show #2

> close #3

> surface #2 sharpBoundaries false

> hide #2

> mlp #1 surfaces #2

Map values for surface "Tunnel 1_A SES surface": minimum inf, mean inf,
maximum inf  
Map values for surface "Tunnel 2_A SES surface": minimum inf, mean inf,
maximum inf  

> usage surface

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 invertShown
  * surface showall
  * surface showPatches
  * surface splitbycolor
  * surface squaremesh
  * surface style
  * surface transform
  * surface undust
  * surface unzone
  * surface zone

  

> surface splitbycolor #2.1

> hide #3.1 models

> show #3.1 models

> hide #!2 models

> hide #3.1 models

> show #3.1 models

> mlp #1 surfaces #3

Map values for surface "piece 1": minimum -14.57, mean 1.974, maximum 17.72  

> close #3

> surface splitbycolor #2

> mlp #1 surfaces #3,4

Map values for surface "piece 1": minimum -14.57, mean 1.974, maximum 17.72  
Map values for surface "piece 1": minimum -16.48, mean -0.8182, maximum 15.48  

> lighting simple

> set bgColor white

> set bgColor #ffffff00

> lighting full

> lighting simple

> save /Users/goddard/Desktop/image1.png supersample 3

> set bgColor black

> set bgColor transparent

> save /Users/goddard/Desktop/image2.png supersample 3

> mlp #1 surfaces #3,4 range -10,10

Map values for surface "piece 1": minimum -14.57, mean 1.974, maximum 17.72  
Map values for surface "piece 1": minimum -16.48, mean -0.8182, maximum 15.48  

> save /Users/goddard/Desktop/image3.png supersample 3

> set bgColor gray

> set bgColor #80808000

> set bgColor white

> set bgColor #ffffff00

> save /Users/goddard/Desktop/image4.png supersample 3

> mlp #1 surfaces #3,4 range -5,5

Map values for surface "piece 1": minimum -14.57, mean 1.974, maximum 17.72  
Map values for surface "piece 1": minimum -16.48, mean -0.8182, maximum 15.48  

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> save /Users/goddard/Desktop/image5.png supersample 3

> set bgColor black

> set bgColor transparent

> save /Users/goddard/Desktop/image6.png supersample 3




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 451.140.1.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 22 days 22:40

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          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
    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-ArtiaX: 0.1
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202210132007
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.1
    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: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.0.6
    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-PhenixUI: 1.0.1
    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: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    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
    pandas: 1.4.4
    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: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.4
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.1
    starfile: 0.4.11
    superqt: 0.3.5
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1

[Tom Goddard]

Fixed in 1.5 and daily builds.

Made mlp command use the specified atoms for coloring surfaces given with the surface option which have no atoms in common with the specified atoms.