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#6524 closed defect (duplicate)
Loss of occupancy/bfactor
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | 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: 1.4.dev202202040724 (2022-02-04 07:24:35 UTC)
Description
Hi,
Thanks for actively developing this great piece of software! I encountered what I think is a bug.
When saving a pdb file chimeraX sets accupancy & B-factors of all atoms to 0! I can't imagine that this is the intended behavior, since it represents a loss of information and leads to a lot of problems in downstream applications in other software. In addition, also the space group information ('P 1' on the CRYST1 line) is lost after saving.
here snippets from two pdb files, before and after saving in chimeraX (literaly just opened the pdb and then saved it immediately):
BEFORE:
"HELIX 1 1 HIS A 32 MET A 35 1 4
CRYST1 396.000 396.000 396.000 90.00 90.00 90.00 P 1
ATOM 1 N ASN A 31 207.656 273.296 178.276 1.00 30.00 N
ATOM 2 CA ASN A 31 209.106 273.230 178.470 1.00 30.00 C
ATOM 3 C ASN A 31 209.615 271.997 177.753 1.00 30.00 C
ATOM 4 O ASN A 31 210.628 272.124 177.095 1.00 30.00 O
ATOM 5 CB ASN A 31 209.476 273.204 179.954 1.00 30.00 C
ATOM 6 CG ASN A 31 209.279 274.547 180.628 1.00 30.00 C
ATOM 7 OD1 ASN A 31 209.276 275.589 179.973 1.00 30.00 O
ATOM 8 ND2 ASN A 31 209.113 274.529 181.946 1.00 30.00 N"
AFTER SAVING:
"SEQRES 1 A 9 ASN HIS ASP ASN MET CYS LYS VAL LYS
HELIX 1 1 HIS A 32 MET A 35 1 4
CRYST1 396.000 396.000 396.000 90.00 90.00 90.00
ATOM 1 N ASN A 31 207.656 273.296 178.276 0.00 0.00 N
ATOM 2 CA ASN A 31 209.106 273.230 178.470 0.00 0.00 C
ATOM 3 C ASN A 31 209.615 271.997 177.753 0.00 0.00 C
ATOM 4 O ASN A 31 210.628 272.124 177.095 0.00 0.00 O
ATOM 5 CB ASN A 31 209.476 273.204 179.954 0.00 0.00 C
ATOM 6 CG ASN A 31 209.279 274.547 180.628 0.00 0.00 C
ATOM 7 OD1 ASN A 31 209.276 275.589 179.973 0.00 0.00 O
ATOM 8 ND2 ASN A 31 209.113 274.529 181.946 0.00 0.00 N"
Best,
Moritz
OpenGL version: 4.1 INTEL-12.10.31
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.
Locale: UTF-8
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac16,2
Processor Name: Intel Core i5
Processor Speed: 3.1 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 16 GB
Boot ROM Version: 427.140.8.0.0
SMC Version (system): 2.32f20
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G9323)
Kernel Version: Darwin 18.7.0
Time since boot: 46 days 1:57
Graphics/Displays:
Intel Iris Pro Graphics 6200:
Chipset Model: Intel Iris Pro Graphics 6200
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1622
Revision ID: 0x000a
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
DELL P2217H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 668VC77B81AB
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DisplayPort
HP E190i:
Resolution: 1280 x 1024 (SXGA - Super eXtended Graphics Array)
UI Looks like: 1280 x 1024 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: CN47280B9M
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
iMac:
Display Type: Built-In Retina LCD
Resolution: 4096 x 2304 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 678221B832F23
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.5.30
cftime: 1.5.2
charset-normalizer: 2.0.11
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.35.1
ChimeraX-AtomicLibrary: 5.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202202040724
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.6
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.1
ChimeraX-ModelPanel: 1.3.1
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: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.7.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1
ChimeraX-VIPERdb: 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: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.5.1
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.29.1
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.26
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.0.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.0
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.26
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.2.2
QtPy: 2.0.1
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
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
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.8
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Attachments (2)
Change History (7)
comment:1 by , 4 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Loss of occupancy/bfactor |
comment:2 by , 4 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 4 years ago
Hi Eric, thanks for looking into this!
It is indeed more complicated than I thought, it does not happen every time. Took me a while, but I found a way to reproduce it using 1gcn:
* I start with a fresh session (‘close session’)
* ‘open 1gcn’
* Save it (‘1gcn_saved.pdb’)
* Open the just saved model
* Save it again (‘1gcn_saved_again.pdb’)
The first one will have the occupancy & bfactors normal, the second one will have them all set to 0. I’m on my laptop right now, but the original bug report was from my work desktop. On my laptop I am running the (I think) latest version, with the tile function -> 1.4.dev202202040724 (2022-02-04). I am pretty sure it’s the same version on my desktop. Below the log of my commands and attached the two pdb files. I saved it through the menu, but from the log file you see differences in the commands: and when saving the first time it is ‘relModel #1’ and when saving the second time, since there are two open models now, it’s saving with ‘models #2’ and not relModel. Also, there are warning when opening the pdb.
Best,
Moritz
-----
close session
open 1gcn
1gcn title:
X-ray analysis of glucagon and its relationship to receptor binding [more info...]
Chain information for 1gcn #1
Chain Description UniProt
A glucagon GLUC_PIG
save /Users/moritzhunkeler/Desktop/1gcn_saved.pdb relModel #1
open /Users/moritzhunkeler/Desktop/1gcn_saved.pdb
Summary of feedback from opening /Users/moritzhunkeler/Desktop/1gcn_saved.pdb
warnings Ignored bad PDB record found on line 4
Ignored bad PDB record found on line 253
Chain information for 1gcn_saved.pdb #2
Chain Description
A No description available
save /Users/moritzhunkeler/Desktop/1gcn_saved_again.pdb models #2
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, April 4, 2022 at 12:54
To:
Cc: mhunkeler@crystal.harvard.edu <mhunkeler@crystal.harvard.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #6524: Loss of occupancy/bfactor
#6524: Loss of occupancy/bfactor
-----------------------------------+----------------------
Reporter: mhunkeler@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------+----------------------
Changes (by pett):
* status: accepted => feedback
Comment:
Hi Moritz,
Thanks for reporting this problem. A simple test did not
reproduce it for me. Can you try opening 1gcn and saving it? Do the
occupancy/bfactors get zeroed out or do they keep their values? If the
former, then try updating your ChimeraX. If the latter, then there's
something specific about your PDB file that's making this happen, and I
would need access to it (or at least part of it) to track this down.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6524#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | feedback → closed |
Hi Moritz,
Update your version of ChimeraX. There was a period of 11 days (2/2-2/12, your current ChimeraX is from 2/4) where there was a chance that files with a .pdb suffix would be read by the ZDOCK file reader (which also uses the .pdb suffix) instead of the regular PDB file reader. The ZDOCK reader doesn't use/read the occupancy/bfactor columns. Sorry but it took me awhile to recollect that bug/fix.
If for some reason you can't upgrade right now, you can ensure that a file is read by the normal PDB reader by adding "format pdb" to the open command.
--Eric
comment:5 by , 4 years ago
Omg how unlucky.
Thanks a lot!
Moritz
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, April 4, 2022 at 20:20
To:
Cc: mhunkeler@crystal.harvard.edu <mhunkeler@crystal.harvard.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #6524: Loss of occupancy/bfactor
#6524: Loss of occupancy/bfactor
-----------------------------------+--------------------
Reporter: mhunkeler@… | Owner: pett
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: duplicate | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------+--------------------
Changes (by pett):
* status: feedback => closed
* resolution: => duplicate
Comment:
Hi Moritz,
Update your version of ChimeraX. There was a period of 11 days
(2/2-2/12, your current ChimeraX is from 2/4) where there was a chance
that files with a .pdb suffix would be read by the ZDOCK file reader
(which also uses the .pdb suffix) instead of the regular PDB file reader.
The ZDOCK reader doesn't use/read the occupancy/bfactor columns. Sorry
but it took me awhile to recollect that bug/fix.
If for some reason you can't upgrade right now, you can ensure
that a file is read by the normal PDB reader by adding "format pdb" to the
open command.
--Eric
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6524#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
Note:
See TracTickets
for help on using tickets.
Hi Moritz,
--Eric