Opened 3 years ago
Last modified 3 years ago
#8525 assigned defect
Session restore: Compressed file ended before the end-of-stream marker was reached
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.17763
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/AYGroupUser/Desktop/DBA/ppts/PG_HELIX_RED.cxs
Log from Sat Mar 5 16:13:27 2022 Startup Messages
---
warning | Your computer has Intel graphics driver 7642 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/Samia/Desktop/pg83_sites.pdb
Chain information for pg83_sites.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
2v | No description available
2w | No description available
2x | No description available
2y | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | 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
h | No description available
> show cartoons
> hide atoms
> set bgColor white
> graphics silhouettes true
> lighting soft
> lighting simple
> hide #1.1 models
> cartoon style nucleic xsection round width 1 thickness 0.8
> select /A
50909 atoms, 57000 bonds, 31 pseudobonds, 2372 residues, 2 models selected
> select ~sel
29844 atoms, 29887 bonds, 11 pseudobonds, 4219 residues, 2 models selected
> hide sel cartoons
> select /A
50909 atoms, 57000 bonds, 31 pseudobonds, 2372 residues, 2 models selected
> color #1 royalblue transparency 0
> cartoon style nucleic xsection round width 1 thickness 1.2
> select clear
> select /A
50909 atoms, 57000 bonds, 31 pseudobonds, 2372 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light steel blue
> select clear
> select #2/a: 155-170, 605-620, 1215-1230, 1725-1735, 1865-1875, 2205-2220
Nothing selected
> open C:/Users/Samia/Desktop/7k00_e_coli.pdb
Summary of feedback from opening C:/Users/Samia/Desktop/7k00_e_coli.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 AC5 2 VAL X
3 LYS X 5 0
Start residue of secondary structure not found: SHEET 2 AC5 2 VAL X 17 VAL X
19 -1
Start residue of secondary structure not found: SHEET 1 AC6 2 LEU X 34 LYS X
36 0
Start residue of secondary structure not found: SHEET 2 AC6 2 ALA X 61 ARG X
63 -1
Start residue of secondary structure not found: SHEET 1 AC7 4 ARG X 101 LEU X
105 0
43 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 AD9 3 ARG B 95 LYS B 99
0
Start residue of secondary structure not found: SHEET 2 AD9 3 VAL B 102 SER B
106 -1
Start residue of secondary structure not found: SHEET 3 AD9 3 VAL B 113 GLN B
116 -1
Start residue of secondary structure not found: SHEET 1 AE1 3 GLN C 18 ASN C
20 0
Start residue of secondary structure not found: SHEET 2 AE1 3 GLN C 2 ILE C 4
-1
Start residue of secondary structure not found: SHEET 3 AE1 3 VAL C 37 PRO C
38 -1
24 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 AE8 3 VAL F 89 VAL F 90
0
Start residue of secondary structure not found: SHEET 2 AE8 3 THR F 121 VAL F
122 1
Start residue of secondary structure not found: SHEET 3 AE8 3 LYS F 141 ILE F
142 1
Start residue of secondary structure not found: SHEET 1 AE9 4 LYS G 62 ILE G
65 0
Start residue of secondary structure not found: SHEET 2 AE9 4 VAL G 101 ASP G
106 -1
Start residue of secondary structure not found: SHEET 3 AE9 4 PHE G 31 ALA G
35 -1
7 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 AF3 4 VAL I 47 SER I 52
0
Start residue of secondary structure not found: SHEET 2 AF3 4 ILE I 35 ILE I
40 -1
Start residue of secondary structure not found: SHEET 3 AF3 4 ARG I 25 ARG I
30 -1
Start residue of secondary structure not found: SHEET 4 AF3 4 SER I 91 ASP I
93 1
End residue of secondary structure not found: SHEET 1 AF4 4 LYS L 10 VAL L 14
0
Start residue of secondary structure not found: SHEET 2 AF4 4 TYR L 2 SER L 7
-1
Start residue of secondary structure not found: SHEET 3 AF4 4 VAL L 38 ALA L
42 -1
Start residue of secondary structure not found: SHEET 4 AF4 4 VAL L 47 ILE L
49 -1
Start residue of secondary structure not found: SHEET 1 AF5 4 THR L 19 LEU L
22 0
Start residue of secondary structure not found: SHEET 2 AF5 4 TRP L 92 SER L
102 -1
37 messages similar to the above omitted
End residue of secondary structure not found: SHEET 3 AG7 4 ARG Q 77 GLU Q 83
-1
Start residue of secondary structure not found: SHEET 4 AG7 4 HIS Q 46 ALA Q
47 1
Start residue of secondary structure not found: SHEET 1 AG8 2 VAL R 13 ARG R
18 0
Start residue of secondary structure not found: SHEET 2 AG8 2 ALA R 24 PHE R
29 -1
Start residue of secondary structure not found: SHEET 1 AG9 2 LEU R 33 VAL R
40 0
Start residue of secondary structure not found: SHEET 2 AG9 2 ARG R 45 SER R
52 -1
21 messages similar to the above omitted
Chain information for 7k00_e_coli.pdb #2
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
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
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
> hide #!1 models
> show #!2 cartoons
> hide #!2 atoms
> select #2/a
63520 atoms, 66364 bonds, 3 pseudobonds, 7004 residues, 2 models selected
> select ~sel
166571 atoms, 174613 bonds, 46 pseudobonds, 17306 residues, 4 models selected
> hide sel & #!2 cartoons
> show #!1 models
> hide #!1 models
> select #2/a: 155-170, 605-620, 1215-1230, 1725-1735, 1865-1875, 2205-2220
1844 atoms, 2058 bonds, 86 residues, 1 model selected
> color sel red
> select #2/a: 155-170, 605-620, 1215-1230, 1725-1735, 1865-1875, 2205-2220,
> 2790-2805
2182 atoms, 2434 bonds, 102 residues, 1 model selected
> color sel red
> select clear
> cartoon style nucleic xsection round width 1 thickness 1.2
> show #!1 models
> hide #2.1 models
> ui tool show Matchmaker
> matchmaker #2/a to #1/A pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pg83_sites.pdb, chain A (#1) with 7k00_e_coli.pdb, chain a (#2),
sequence alignment score = 5842.8
RMSD between 822 pruned atom pairs is 1.481 angstroms; (across all 2329 pairs:
8.633)
> color #1 #61aede transparency 0
> color #1 #8a60de transparency 0
> color #1 #48a5de transparency 0
> color #1 #60b2de transparency 0
> color #1 #dedbc9 transparency 0
> color #1 #dedede transparency 0
> color #1 #dec9b9 transparency 0
> color #1 #dec0b1 transparency 0
> select #2/a: 155-170, 605-620, 1215-1230, 1725-1735, 1865-1875, 2205-2220,
> 2790-2805
2182 atoms, 2434 bonds, 102 residues, 1 model selected
> select clear
> color #2 #b6c8f4 transparency 0
> color #2 #91aff4 transparency 0
> color #2 #f480d1 transparency 0
> color #2 salmon transparency 0
> color #1 royalblue transparency 0
> select #2/a: 155-170, 605-620, 1215-1230, 1725-1735, 1865-1875, 2205-2220,
> 2790-2805
2182 atoms, 2434 bonds, 102 residues, 1 model selected
> color sel red
> color sel lime
> ui tool show "Color Actions"
> color sel dark olive green
[Repeated 1 time(s)]
> color sel medium spring green
> color sel green
> color sel green yellow
> color sel cyan
> color sel sandy brown
> color sel light blue
> color sel violet
> color sel dark red
> color sel red
> color sel salmon
> color sel dark blue
> color sel medium blue
> color sel magenta
> color sel deep pink
> color sel light coral
> color sel dark sea green
> color sel light green
> select clear
> hide #!1 models
> show #!1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> select #1/A: 626-644, 1858-1902, 2210-2224, 138-153, 1241-1258, 1744-1758
1848 atoms, 2061 bonds, 4 pseudobonds, 86 residues, 2 models selected
> color (#!1 & sel) red
> hide #!2 models
> select ~sel
228243 atoms, 238916 bonds, 45 pseudobonds, 24224 residues, 4 models selected
> ui tool show "Color Actions"
> color sel light steel blue
> select clear
> hide #1.1 models
> save C:/Users/Samia/Desktop/10_02_22/PG_HELIX_RED.cxs
——— End of log from Sat Mar 5 16:13:27 2022 ———
opened ChimeraX session
> cartoon style nucleic xsection round width 1.6 thickness 0.7
> cartoon style nucleic xsection round width 1.6 thickness 1.0
> cartoon style nucleic xsection round width 1.6 thickness 1.5
> cartoon style nucleic xsection round width 2.0 thickness 1.5
> select clear
> save C:/Users/AYGroupUser/Desktop/DBA/ppts/helix_red_1.jpg width 701 height
> 460 supersample 3
> close session
> open C:/Users/AYGroupUser/Desktop/DBA/ppts/helix10.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 708, in restore
data = fdeserialize(stream)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 70, in msgpack_deserialize
return next(stream)
File "msgpack\\_unpacker.pyx", line 540, in
msgpack._cmsgpack.Unpacker.__next__
File "msgpack\\_unpacker.pyx", line 474, in msgpack._cmsgpack.Unpacker._unpack
File "msgpack\\_unpacker.pyx", line 448, in
msgpack._cmsgpack.Unpacker.read_from_file
File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 668, in read
return self._buffer.read(size)
File "C:\Program Files\ChimeraX\bin\lib\\_compression.py", line 68, in
readinto
data = self.read(len(byte_view))
File "C:\Program Files\ChimeraX\bin\lib\\_compression.py", line 99, in read
raise EOFError("Compressed file ended before the "
EOFError: Compressed file ended before the end-of-stream marker was reached
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 512.36
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1255
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Latitude 5401
OS: Microsoft Windows 10 Enterprise LTSC (Build 17763)
Memory: 34,131,316,736
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9850H CPU @ 2.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
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: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
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
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: 1.1.2
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-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: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
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
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
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: 5.1.0
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: 5.1.0
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: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
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: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
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: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (1)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session restore: Compressed file ended before the end-of-stream marker was reached |
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Reported by Disha Hiregange