Opened 5 years ago

Closed 5 years ago

#4145 closed defect (fixed)

Floating point 'increment' not allowed in "volume planes" command despite documentation to the contrary

Reported by: ermel@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version: 1.1
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-1103-oem-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Hi, 

I encountered a bug using the "volume planes" command. The documentation states: 

" The start, end, increment, and depth parameters can be floating-point numbers. For example, an increment of 0.25 with step size 1 will show each plane for 4 frames.". 

I wanted to make use of that while making a movie and slowly loop through a volume at stepsize 1 with floating point increments, but when using floating point increments, the command fails with: 

"Invalid "planes" argument: Planes arguments after axis must be integers"

An example cxc-file is attached for reproduction. This is caused by the PlanesArg-class from volumecommand.py in the map-bundle trying to convert the input string to integers. When converting to floats instead it works as expected. 

Best,
Utz Ermel

Log:
> open 6ztm

Summary of feedback from opening 6ztm fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "PHE" near line 199412  
  
6ztm title:  
E. coli 70S-RNAP expressome complex in collided state without NusG [more
info...]  
  
Chain information for 6ztm #1  
---  
Chain | Description  
AA | 16S ribosomal RNA  
AB | 30S ribosomal protein S2  
AC | 30S ribosomal protein S3  
AD | 30S ribosomal protein S4  
AE | 30S ribosomal protein S5  
AF | 30S ribosomal protein S6  
AG | 30S ribosomal protein S7  
AH | 30S ribosomal protein S8  
AI | 30S ribosomal protein S9  
AJ | 30S ribosomal protein S10  
AK | 30S ribosomal protein S11  
AL | 30S ribosomal protein S12  
AM | 30S ribosomal protein S13  
AN | 30S ribosomal protein S14  
AO | 30S ribosomal protein S15  
AP | 30S ribosomal protein S16  
AQ | 30S ribosomal protein S17  
AR | 30S ribosomal protein S18  
AS | 30S ribosomal protein S19  
AT | 30S ribosomal protein S20  
AU | 30S ribosomal protein S21  
AV | mRNA  
AW | tRNA(fmet) P-site  
AX | Phe-NH-tRNA(Phe) A-site  
B1 | 50S ribosomal protein L30  
B2 | 50S ribosomal protein L32  
B3 | 50S ribosomal protein L33  
B4 | 50S ribosomal protein L34  
B5 | 50S ribosomal protein L35  
B6 | 50S ribosomal protein L36  
BA | 23S ribosomal RNA  
BB | 5S ribosomal RNA  
BC | 50S ribosomal protein L2  
BD | 50S ribosomal protein L3  
BE | 50S ribosomal protein L4  
BF | 50S ribosomal protein L5  
BG | 50S ribosomal protein L6  
BH | 50S ribosomal protein L9  
BK | 50S ribosomal protein L13  
BL | 50S ribosomal protein L14  
BM | 50S ribosomal protein L15  
BN | 50S ribosomal protein L16  
BO | 50S ribosomal protein L17  
BP | 50S ribosomal protein L18  
BQ | 50S ribosomal protein L19  
BR | 50S ribosomal protein L20  
BS | 50S ribosomal protein L21  
BT | 50S ribosomal protein L22  
BU | 50S ribosomal protein L23  
BV | 50S ribosomal protein L24  
BW | 50S ribosomal protein L25  
BX | 50S ribosomal protein L27  
BY | 50S ribosomal protein L28  
BZ | 50S ribosomal protein L29  
CA CB | DNA-directed RNA polymerase subunit α  
CC | DNA-directed RNA polymerase subunit β  
CD | DNA-directed RNA polymerase subunit beta'  
CN | Non-template DNA strand  
CT | Template DNA strand  
  
Non-standard residues in 6ztm #1  
---  
3AU — 3-[(3S)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate) (None)  
3TD —
(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-
D-ribitol  
4D4 — (2S,3R)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid  
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid  
MG — magnesium ion  
ZN — zinc ion  
  

> molmap #1 20

> hide #1

> volume onesmask #2

> hide #2

> volume #3 step 1 color white backingColor black planes z,1 style image
> imageMode "full region"

> volume #3 planes z,1,60,1

> volume #3 planes z,1,60,0.5

Invalid "planes" argument: Planes arguments after axis must be integers  




OpenGL version: 3.3.0 NVIDIA 440.100
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 3630 Tower
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 8 Intel(R) Xeon(R) E-2174G CPU @ 3.80GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         45G         14G        398M        3.1G         16G
	Swap:            0B          0B          0B

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P5000] [10de:1bb0] (rev a1)	
	Subsystem: Dell GP104GL [Quadro P5000] [1028:11b2]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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
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    cxservices: 1.0
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    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
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    sfftk-rw: 0.6.6.dev0
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File attachment: planes_bug.cxc

planes_bug.cxc​

Attachments (1)

planes_bug.cxc​ (207 bytes ) - added by ermel@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by ermel@…, 5 years ago

Attachment: planes_bug.cxc​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 years ago

Cc: Elaine Meng added
Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Floating point 'increment' not allowed in "volume planes" command despite documentation to the contrary
Version: → 1.1

Reported by Utz Ermel

comment:2 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in tonight's ChimeraX daily build.

Thanks for the detailed bug report. It was a mistake in the code that it parsed the values as integer instead of float.

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