Opened 4 years ago

Closed 4 years ago

#5272 closed defect (fixed)

ISOLDE: All atoms for zone mask must be from a single model!

Reported by: irisdyoung@… Owned by: Tristan Croll
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-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Fixed atoms to match MODRNA_2MA template and then tried to refine that residue. 

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  
Successfully installed
'ChimeraX_ISOLDE-1.2.2-cp38-cp38-macosx_10_13_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/Users/iris/Library/Caches/ChimeraX/1.2/installers/ChimeraX_ISOLDE-1.2.2-cp38-cp38-macosx_10_13_x86_64.whl  
Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3)  
Requirement already satisfied: ChimeraX-Core~=1.2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5)  
Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in
/Users/iris/Library/Application Support/ChimeraX/1.2/site-packages (from
ChimeraX-ISOLDE==1.2.2) (0.16.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.0.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.4)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.5)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.7.6)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.2)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.3.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
ChimeraX-ISOLDE is already installed with the same version as the provided
wheel. Use --force-reinstall to force an installation of the wheel.  
  

WARNING: You are using pip version 21.0.1; however, version 21.2.4 is
available.  
You should consider upgrading via the
'/Applications/ChimeraX-1.2.5.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.  
  

/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:411: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'AGBNP3':  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:433: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'GVolSA':  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:440: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'AGBNP':  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> open
> /Users/iris/Research/Oxazolidinones/refinement/wt_LZD_stalled/deposition/wt_LZD_stalled_rs6_007_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif

Summary of feedback from opening
/Users/iris/Research/Oxazolidinones/refinement/wt_LZD_stalled/deposition/wt_LZD_stalled_rs6_007_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif  
---  
warnings | Duplicate polymer '19' near line 482155  
Missing entity information. Treating each chain as a separate entity.  
Atom H is not in the residue template for ARG /1:3  
Atom H is not in the residue template for ASN /2:3  
Atom H is not in the residue template for MET /D:9  
Atom H is not in the residue template for GLY /E:2  
Atom H is not in the residue template for ALA /F:2  
1 messages similar to the above omitted  
Atom H5' is not in the residue template for 6MZ /I:1618  
Atom O1P is not in the residue template for PSU /I:1911  
Atom O1P is not in the residue template for PSU /I:1917  
Atom H5' is not in the residue template for 6MZ /I:2030  
Atom H is not in the residue template for ALA /K:2  
Atom H is not in the residue template for ALA /N:2  
Atom H is not in the residue template for SER /O:2  
Atom HN1 is not in the residue template for 4D4 /U:81  
Atom H is not in the residue template for ASP /W:2  
Atom H is not in the residue template for SER /X:2  
Atom H is not in the residue template for ALA /Y:2  
Atom H is not in the residue template for ALA /c:2  
Atom H is not in the residue template for ARG /e:11  
15 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
notes | Fetching CCD 1MG from http://ligand-
expo.rcsb.org/reports/1/1MG/1MG.cif  
Fetching CCD 5MU from http://ligand-expo.rcsb.org/reports/5/5MU/5MU.cif  
Fetching CCD 6MZ from http://ligand-expo.rcsb.org/reports/6/6MZ/6MZ.cif  
Fetching CCD 2MG from http://ligand-expo.rcsb.org/reports/2/2MG/2MG.cif  
Fetching CCD 3TD from http://ligand-expo.rcsb.org/reports/3/3TD/3TD.cif  
Fetching CCD 5MC from http://ligand-expo.rcsb.org/reports/5/5MC/5MC.cif  
Fetching CCD G7M from http://ligand-expo.rcsb.org/reports/G/G7M/G7M.cif  
Fetching CCD OMG from http://ligand-expo.rcsb.org/reports/O/OMG/OMG.cif  
Fetching CCD H2U from http://ligand-expo.rcsb.org/reports/H/H2U/H2U.cif  
Fetching CCD OMC from http://ligand-expo.rcsb.org/reports/O/OMC/OMC.cif  
Fetching CCD 2MA from http://ligand-expo.rcsb.org/reports/2/2MA/2MA.cif  
Fetching CCD OMU from http://ligand-expo.rcsb.org/reports/O/OMU/OMU.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
Fetching CCD 4D4 from http://ligand-expo.rcsb.org/reports/4/4D4/4D4.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD ZLD from http://ligand-expo.rcsb.org/reports/Z/ZLD/ZLD.cif  
  
Chain information for
wt_LZD_stalled_rs6_007_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif
#1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
A | 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  
  
Chain information for
wt_LZD_stalled_rs6_007_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif  
---  
Chain | Description  
1.2/1 | No description available  
1.2/2 | No description available  
1.2/3 | No description available  
1.2/4 | No description available  
1.2/A | 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  
  

> open
> /Users/iris/Research/Oxazolidinones/maps/WT_LZD_stalled/70S_wt_Ldz_stall_248_512_unsharpened_volume50_updatedpixelsize.mrc

Opened 70S_wt_Ldz_stall_248_512_unsharpened_volume50_updatedpixelsize.mrc as
#2, grid size 512,512,512, pixel 0.812, shown at level 2.63, step 2, values
float32  
Opened 70S_wt_Ldz_stall_248_512_unsharpened_volume50_updatedpixelsize.mrc as
#1.1.1.1, grid size 512,512,512, pixel 0.812, shown at step 1, values float32  

> view #1.2/4

> volume #1.1.1.1 level 2.37

> volume #1.1.1.1 level 3.946

> view #1.2/5

> ui windowfill toggle

> volume #1.1.1.1 level 2.058

> volume #1.1.1.1 level 0.987

> volume #1.1.1.1 level 3.078

> view /U:2506

No objects specified.  

> view /I:2506

Loading residue template for ZLD from internal database  
ISOLDE: stopped sim  

Populating font family aliases took 1058 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: stopped sim  

> view /I:2585

> view /I:2585

ISOLDE: started sim  
ISOLDE: stopped sim  

> volume #1.1.1.1 level 1.5

ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  

> ui tool show "Build Structure"

> build start atom #1.2 res MG

> build modify /het:1@He Mg 0 name Mg

ISOLDE: stopped sim  

> select clear

ISOLDE: stopped sim  

> select clear

> ui mousemode right "translate selected atoms"

> select clear

> ui mousemode right translate

> view /I:2585

> view /I:2506

> view /I:2602

> build start atom #1.2 res MG

> build modify /het:2@He Mg 0 name Mg

> save
> /Users/iris/Research/Oxazolidinones/refinement/wt_LZD_stalled/wt_LZD_stalled_rs6_007_metals_adjusted_ISOLDE_fixed_manually_edited_extracted_biology_edited.pdb
> #1.2

> view /5

> close #1

> open
> /Users/iris/Research/Oxazolidinones/maps/WT_LZD/70S_wt_Ldz_235_512_unsharpened_volume_29_updatedpixelsize.mrc

Opened 70S_wt_Ldz_235_512_unsharpened_volume_29_updatedpixelsize.mrc as #1,
grid size 512,512,512, pixel 0.812, shown at level 2.57, step 2, values
float32  

> open
> /Users/iris/Research/Oxazolidinones/refinement/wt_LZD/deposition/wt_LZD_rs1_005_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif

Summary of feedback from opening
/Users/iris/Research/Oxazolidinones/refinement/wt_LZD/deposition/wt_LZD_rs1_005_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for ARG /1:3  
Atom H is not in the residue template for ASN /2:3  
Atom H is not in the residue template for MET /D:9  
Atom H is not in the residue template for GLY /E:2  
Atom H is not in the residue template for ALA /F:2  
1 messages similar to the above omitted  
Atom H5' is not in the residue template for 6MZ /I:1618  
Atom O1P is not in the residue template for PSU /I:1911  
Atom O1P is not in the residue template for PSU /I:1917  
Atom H5' is not in the residue template for 6MZ /I:2030  
Atom H is not in the residue template for ALA /K:2  
Atom H is not in the residue template for ALA /N:2  
Atom H is not in the residue template for SER /O:2  
Atom H is not in the residue template for ASP /W:2  
Atom H is not in the residue template for SER /X:2  
18 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for
wt_LZD_rs1_005_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | 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  
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  
  
Chain information for
wt_LZD_rs1_005_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif  
---  
Chain | Description  
2.2/1 | No description available  
2.2/2 | No description available  
2.2/3 | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
2.2/F | No description available  
2.2/G | No description available  
2.2/H | No description available  
2.2/I | No description available  
2.2/J | No description available  
2.2/K | No description available  
2.2/L | No description available  
2.2/M | No description available  
2.2/N | No description available  
2.2/O | No description available  
2.2/P | No description available  
2.2/Q | No description available  
2.2/R | No description available  
2.2/S | No description available  
2.2/T | No description available  
2.2/U | No description available  
2.2/V | No description available  
2.2/W | No description available  
2.2/X | No description available  
2.2/Y | No description available  
2.2/Z | No description available  
2.2/a | No description available  
2.2/b | No description available  
2.2/c | No description available  
2.2/d | No description available  
2.2/e | No description available  
2.2/f | No description available  
2.2/g | No description available  
2.2/h | No description available  
2.2/i | No description available  
2.2/j | No description available  
2.2/k | No description available  
2.2/l | No description available  
2.2/m | No description available  
2.2/n | No description available  
2.2/o | No description available  
2.2/p | No description available  
2.2/q | No description available  
2.2/r | No description available  
2.2/t | No description available  
2.2/u | No description available  
2.2/v | No description available  
2.2/w | No description available  
2.2/x | No description available  
2.2/y | No description available  
2.2/z | No description available  
  
Opened 70S_wt_Ldz_235_512_unsharpened_volume_29_updatedpixelsize.mrc as
#2.1.1.1, grid size 512,512,512, pixel 0.812, shown at step 1, values float32  

> ui windowfill toggle

> view /m:2062

No objects specified.  

> view /I:2062

> volume #2.1.1.1 level 2.033

> ui tool show "Build Structure"

> select clear

> view /I:2506

ISOLDE: started sim  
ISOLDE: stopped sim  

> volume #2.1.1.1 level 0.9112

> view /I:2602

> volume #2.1.1.1 level 0.2179

> volume #2.1.1.1 level 1.313

> view /I:2584

> volume #2.1.1.1 level 2.915

> open
> /Users/iris/Research/Oxazolidinones/refinement/wt_LZD_stalled/wt_LZD_stalled_rs6_007_metals_adjusted_ISOLDE_fixed_manually_edited_extracted_biology_edited_renamedZLDatoms.pdb

Chain information for
wt_LZD_stalled_rs6_007_metals_adjusted_ISOLDE_fixed_manually_edited_extracted_biology_edited_renamedZLDatoms.pdb
#1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
A | 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  
  

> select clear

> style stick

Changed 479087 atom styles  

> volume #2.1.1.1 level 0.8719

ISOLDE: started sim  
ISOLDE: stopped sim  

> view /5

> build start atom #2.2 res MG

> build modify #2.2/het:1@He Mg 0 name Mg

> view /I:2602

> build start atom #2.2 res MG

> build modify #2.2/het:2@He Mg 0 name Mg

> view /I:2602

> select #1

240911 atoms, 253212 bonds, 3 pseudobonds, 10540 residues, 2 models selected  

> select #2.2

238178 atoms, 250269 bonds, 3 pseudobonds, 10458 residues, 12 models selected  

> show sel atoms

> volume #2.1.1.1 level 2.471

> select clear

> save
> /Users/iris/Research/Oxazolidinones/refinement/wt_LZD/wt_LZD_rs1_005_metals_adjusted_ISOLDE_fixed_manually_edited_extracted_biology_edited.pdb
> #2.2

> close #1

> close #2

> open
> /Users/iris/Research/Oxazolidinones/refinement/wt_RZD_stalled/deposition/wt_RZD_stalled_rs8_010_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif

Summary of feedback from opening
/Users/iris/Research/Oxazolidinones/refinement/wt_RZD_stalled/deposition/wt_RZD_stalled_rs8_010_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Atom H is not in the residue template for ARG /1:3  
Atom H is not in the residue template for ASN /2:3  
Atom H is not in the residue template for MET /D:9  
Atom H is not in the residue template for GLY /E:2  
Atom H is not in the residue template for ALA /F:2  
1 messages similar to the above omitted  
Atom H5' is not in the residue template for 6MZ /I:1618  
Atom O1P is not in the residue template for PSU /I:1911  
Atom O1P is not in the residue template for PSU /I:1917  
Atom H5' is not in the residue template for 6MZ /I:2030  
Atom H is not in the residue template for ALA /K:2  
Atom H is not in the residue template for ALA /N:2  
Atom H is not in the residue template for SER /O:2  
Atom HN1 is not in the residue template for 4D4 /U:81  
Atom H is not in the residue template for ASP /W:2  
Atom H is not in the residue template for SER /X:2  
Atom H is not in the residue template for ALA /Y:2  
Atom H is not in the residue template for ALA /c:2  
Atom H is not in the residue template for ARG /e:11  
15 messages similar to the above omitted  
Atom C1 is not in the residue template for RD8 /5:1  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
note | Fetching CCD RD8 from http://ligand-expo.rcsb.org/reports/R/RD8/RD8.cif  
  
Chain information for
wt_RZD_stalled_rs8_010_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif
#1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
A | 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  
  
Chain information for
wt_RZD_stalled_rs8_010_metals_adjusted_ISOLDE_fixed_manually_edited_extracted.cif  
---  
Chain | Description  
1.2/1 | No description available  
1.2/2 | No description available  
1.2/3 | No description available  
1.2/4 | No description available  
1.2/A | 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  
  

> view /5

> open
> /Users/iris/Research/Oxazolidinones/maps/WT_RZD_stalled/70S_wt_Rad_stall_248_512_unsharpened_volume46.mrc

Opened 70S_wt_Rad_stall_248_512_unsharpened_volume46.mrc as #2, grid size
512,512,512, pixel 0.825, shown at level 2.95, step 2, values float32  
Opened 70S_wt_Rad_stall_248_512_unsharpened_volume46.mrc as #1.1.1.1, grid
size 512,512,512, pixel 0.825, shown at step 1, values float32  

> volume #1.1.1.1 level 2.44

> volume #1.1.1.1 level 1.048

ISOLDE: stopped sim  

> isolde ignore /5:1 /I:2503 /U:81

ISOLDE: currently ignoring 3 residues in model 1.2  
ISOLDE: started sim  
ISOLDE: stopped sim  

> view /A:2503

No objects specified.  

> view /I:2503

Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2760, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 590, in __init__  
self._prepare_mdff_managers()  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 863, in
_prepare_mdff_managers  
sh.isolate_and_cover_selection(self.sim_construct.mobile_atoms,  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/symmetry.py", line 987, in
isolate_and_cover_selection  
self.map_mgr.cover_atoms(atoms, transforms=transforms,
transform_indices=indices,  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/iris/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
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: 429.140.8.0.0
      SMC Version (system): 2.45f5

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G103)
      Kernel Version: Darwin 18.7.0
      Time since boot: 5 days 5:21

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: (None, '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
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
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Change History (3)

comment:1 by Tom Goddard, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: All atoms for zone mask must be from a single model!

comment:2 by Tristan Croll, 4 years ago

I *think* what happened here is that you tried to start a simulation where (a) the only selected atoms were ignored with isolde ignore, and (b) there were no *non*-ignored atoms close by - so there were no mobile atoms in the simulation construct. The error message that occurs here arises because I was a bit lazy, and only wrote a single generic message for atoms.unique_structures != 1. Have put in a more gentle catch for the case where a selection leads to zero mobile atoms, and also improved upon that error message.

comment:3 by Tristan Croll, 4 years ago

Resolution: → fixed
Status: assigned → closed
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