residue_graph: edges should be a n x 2 array of unsigned ints

[irisdyoung@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Can't fix waters... do they need H on them first?(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open combined_corrected_3.pdb

Chain information for combined_corrected_3.pdb #1  
---  
Chain | Description  
3 | No description available  
4 | No description available  
5 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> isolde start

> set selectionWidth 4

Chain information for combined_corrected_3.pdb  
---  
Chain | Description  
1.2/3 | No description available  
1.2/4 | No description available  
1.2/5 | No description available  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
1.2/J | No description available  
1.2/K | No description available  
1.2/L | No description available  
1.2/M | No description available  
1.2/N | No description available  
1.2/O | No description available  
1.2/P | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/S | No description available  
1.2/T | No description available  
1.2/U | No description available  
1.2/V | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/Z | No description available  
1.2/a | No description available  
1.2/b | No description available  
1.2/c | No description available  
1.2/d | No description available  
1.2/e | No description available  
1.2/f | No description available  
1.2/g | No description available  
1.2/h | No description available  
1.2/i | No description available  
1.2/j | No description available  
1.2/k | No description available  
1.2/l | No description available  
1.2/m | No description available  
1.2/n | No description available  
1.2/o | No description available  
1.2/p | No description available  
1.2/q | No description available  
1.2/r | No description available  
1.2/s | No description available  
1.2/t | No description available  
1.2/u | No description available  
1.2/v | No description available  
1.2/w | No description available  
1.2/x | No description available  
1.2/y | No description available  
1.2/z | No description available  
  
Done loading forcefield  
Loading residue template for ZLD from internal database  
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif  
Deleted the following atoms from residue G 41: OP1  
Fetching CCD SER_LL_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif  
Fetching CCD SER_LL from http://ligand-
expo.rcsb.org/reports/S/SER_LL/SER_LL.cif  
Fetching CCD ALA_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ALA_LEO2/ALA_LEO2.cif  
Fetching CCD SER_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LSN3_DHG/SER_LSN3_DHG.cif  
Fetching CCD ALA_LFZW from http://ligand-
expo.rcsb.org/reports/A/ALA_LFZW/ALA_LFZW.cif  
Fetching CCD PRO_LL from http://ligand-
expo.rcsb.org/reports/P/PRO_LL/PRO_LL.cif  
Fetching CCD CYS_LL_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif  
Fetching CCD THR_LL_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LL_DHG1/THR_LL_DHG1.cif  
Fetching CCD SER_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2_DHG/SER_LEO2_DHG.cif  
Fetching CCD CYS_LL from http://ligand-
expo.rcsb.org/reports/C/CYS_LL/CYS_LL.cif  
Fetching CCD THR_LL from http://ligand-
expo.rcsb.org/reports/T/THR_LL/THR_LL.cif  
Fetching CCD VAL_LL from http://ligand-
expo.rcsb.org/reports/V/VAL_LL/VAL_LL.cif  
Fetching CCD SER_LEO2 from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2/SER_LEO2.cif  
Fetching CCD CYS_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LSN3_DHG/CYS_LSN3_DHG.cif  
Fetching CCD THR_LSN3_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LSN3_DHG1/THR_LSN3_DHG1.cif  
Fetching CCD SER_LFZW_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW_DHG/SER_LFZW_DHG.cif  
Fetching CCD SER_LFZW from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW/SER_LFZW.cif  
Fetching CCD PCA from http://ligand-expo.rcsb.org/reports/P/PCA/PCA.cif  
Fetching CCD ASP_LL_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LL_DHD2/ASP_LL_DHD2.cif  
Fetching CCD ASP_LL from http://ligand-
expo.rcsb.org/reports/A/ASP_LL/ASP_LL.cif  
Fetching CCD PRO_LEO2 from http://ligand-
expo.rcsb.org/reports/P/PRO_LEO2/PRO_LEO2.cif  
Fetching CCD HY3 from http://ligand-expo.rcsb.org/reports/H/HY3/HY3.cif  
Fetching CCD CYS_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2_DHG/CYS_LEO2_DHG.cif  
Fetching CCD ASP_LSN3_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LSN3_DHD2/ASP_LSN3_DHD2.cif  
Fetching CCD AYA from http://ligand-expo.rcsb.org/reports/A/AYA/AYA.cif  
Fetching CCD THR_LEO2_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2_DHG1/THR_LEO2_DHG1.cif  
Fetching CCD LEU_LL from http://ligand-
expo.rcsb.org/reports/L/LEU_LL/LEU_LL.cif  
Fetching CCD CYS_LEO2 from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2/CYS_LEO2.cif  
Fetching CCD THR_LEO2 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2/THR_LEO2.cif  
Fetching CCD VAL_LEO2 from http://ligand-
expo.rcsb.org/reports/V/VAL_LEO2/VAL_LEO2.cif  
Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif  
Fetching CCD PRO_LFZW from http://ligand-
expo.rcsb.org/reports/P/PRO_LFZW/PRO_LFZW.cif  
Fetching CCD THR_LFZW_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW_DHG1/THR_LFZW_DHG1.cif  
Fetching CCD ORN from http://ligand-expo.rcsb.org/reports/O/ORN/ORN.cif  
Fetching CCD CYS_LFZW from http://ligand-
expo.rcsb.org/reports/C/CYS_LFZW/CYS_LFZW.cif  
Fetching CCD THR_LFZW from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW/THR_LFZW.cif  
Fetching CCD VAL_LFZW from http://ligand-
expo.rcsb.org/reports/V/VAL_LFZW/VAL_LFZW.cif  
Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif  
Fetching CCD GMP from http://ligand-expo.rcsb.org/reports/G/GMP/GMP.cif  
Deleted the following atoms from residue G I1025: OP1  
Deleted the following atoms from residue U I2401: OP1  
Fetching CCD ADN from http://ligand-expo.rcsb.org/reports/A/ADN/ADN.cif  
Deleted the following atoms from residue A I2418: OP1  
Deleted the following atoms from residue C I2616: OP1  
Traceback (most recent call last):  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Fetching CCD SAC from http://ligand-expo.rcsb.org/reports/S/SAC/SAC.cif  
Fetching CCD TYR_LL from http://ligand-
expo.rcsb.org/reports/T/TYR_LL/TYR_LL.cif  
Fetching CCD TYR_LEO2 from http://ligand-
expo.rcsb.org/reports/T/TYR_LEO2/TYR_LEO2.cif  
Fetching CCD DAH from http://ligand-expo.rcsb.org/reports/D/DAH/DAH.cif  
Fetching CCD TYR_LFZW from http://ligand-
expo.rcsb.org/reports/T/TYR_LFZW/TYR_LFZW.cif  
Fetching CCD 3NF from http://ligand-expo.rcsb.org/reports/3/3NF/3NF.cif  
Fetching CCD ASP_LEO2_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LEO2_DHD2/ASP_LEO2_DHD2.cif  
Fetching CCD ASP_LFZW_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LFZW_DHD2/ASP_LFZW_DHD2.cif  
Fetching CCD LYS_LL from http://ligand-
expo.rcsb.org/reports/L/LYS_LL/LYS_LL.cif  
Fetching CCD LYS_LL_DHZ3 from http://ligand-
expo.rcsb.org/reports/L/LYS_LL_DHZ3/LYS_LL_DHZ3.cif  
Fetching CCD LYS_LEO2 from http://ligand-
expo.rcsb.org/reports/L/LYS_LEO2/LYS_LEO2.cif  
Fetching CCD MLZ from http://ligand-expo.rcsb.org/reports/M/MLZ/MLZ.cif  
Fetching CCD LYS_LFZW from http://ligand-
expo.rcsb.org/reports/L/LYS_LFZW/LYS_LFZW.cif  
Fetching CCD ALY from http://ligand-expo.rcsb.org/reports/A/ALY/ALY.cif  
Traceback (most recent call last):  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/graph/__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.25
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Intel Core i7
      Processor Speed: 2.9 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: 16 GB
      Boot ROM Version: 429.120.4.0.0
      SMC Version (system): 2.45f0

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9216)
      Kernel Version: Darwin 18.7.0
      Time since boot: 28 days 12:06

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560:

      Chipset Model: Radeon Pro 560
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c0
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AU-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
        DELL U2717D:
          Resolution: 2048 x 1152
          UI Looks like: 2048 x 1152 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 67YGV87DF08L
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
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[Eric Pettersen]

Reported by Iris Young

[Tristan Croll]

Yep - you should always run addh first. I've been meaning to squash that error - comes up when your unrecognised residue doesn't have any bonds (which is of course pretty rare).

[Tristan Croll]

Shouldn't hit this traceback anymore. ISOLDE still won't rebuild residues with fewer than three atoms matching the template, but will raise a UserError with instructions to delete that residue and replace it from scratch. It's also now a bit smarter about detecting missing hydrogens - previously it would only detect if there were *no* hydrogens in the model; now it raises a warning "do you want to run AddH first?" dialogue if (a) the ratio of hydrogens to heavy atoms is less than 1, or (b) any waters have fewer than 3 atoms.