Opened 7 years ago

Closed 7 years ago

#1318 closed defect (fixed)

Apparently bogus help viewer error

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone: 1.0
Component: Documentation Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-4.15.0-34-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.7 (2018-08-07)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.7 (2018-08-07)  
OpenGL version: 3.3.0 NVIDIA 390.48  
OpenGL renderer: Quadro 2000/PCIe/SSE2  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

toolshed show "Blast Protein"

toolshed show "Basic Actions"

help help:quickstart

open 2bbv

Summary of feedback from opening 2bbv fetched from pdb  
---  
notes | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif  
Fetching CCD U from http://ligand-expo.rcsb.org/reports/U/U/U.cif  
Fetching CCD C from http://ligand-expo.rcsb.org/reports/C/C/C.cif  
Fetching CCD A from http://ligand-expo.rcsb.org/reports/A/A/A.cif  
Fetching CCD LEU from http://ligand-expo.rcsb.org/reports/L/LEU/LEU.cif  
Fetching CCD THR from http://ligand-expo.rcsb.org/reports/T/THR/THR.cif  
Fetching CCD ARG from http://ligand-expo.rcsb.org/reports/A/ARG/ARG.cif  
Fetching CCD SER from http://ligand-expo.rcsb.org/reports/S/SER/SER.cif  
Fetching CCD GLN from http://ligand-expo.rcsb.org/reports/G/GLN/GLN.cif  
Fetching CCD PRO from http://ligand-expo.rcsb.org/reports/P/PRO/PRO.cif  
Fetching CCD GLY from http://ligand-expo.rcsb.org/reports/G/GLY/GLY.cif  
Fetching CCD ALA from http://ligand-expo.rcsb.org/reports/A/ALA/ALA.cif  
Fetching CCD PHE from http://ligand-expo.rcsb.org/reports/P/PHE/PHE.cif  
Fetching CCD LYS from http://ligand-expo.rcsb.org/reports/L/LYS/LYS.cif  
Fetching CCD CYS from http://ligand-expo.rcsb.org/reports/C/CYS/CYS.cif  
Fetching CCD ASP from http://ligand-expo.rcsb.org/reports/A/ASP/ASP.cif  
Fetching CCD ASN from http://ligand-expo.rcsb.org/reports/A/ASN/ASN.cif  
Fetching CCD ILE from http://ligand-expo.rcsb.org/reports/I/ILE/ILE.cif  
Fetching CCD GLU from http://ligand-expo.rcsb.org/reports/G/GLU/GLU.cif  
Fetching CCD VAL from http://ligand-expo.rcsb.org/reports/V/VAL/VAL.cif  
Fetching CCD TYR from http://ligand-expo.rcsb.org/reports/T/TYR/TYR.cif  
Fetching CCD TRP from http://ligand-expo.rcsb.org/reports/T/TRP/TRP.cif  
Fetching CCD MET from http://ligand-expo.rcsb.org/reports/M/MET/MET.cif  
Fetching CCD HIS from http://ligand-expo.rcsb.org/reports/H/HIS/HIS.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
Fetching CCD HOH from http://ligand-expo.rcsb.org/reports/H/HOH/HOH.cif  
Used PDBx fixed column width tables to speed up reading mmCIF file  
Used PDBx keywords to speed up reading mmCIF file  
  
Chain information for 2bbv #1  
---  
Chain | Description  
A B C | protein (black beetle virus capsid protein)  
D E F | protein (black beetle virus capsid protein)  
N | RNA (5'-R(*up*cp*up*up*ap*up*ap*up*cp*U)-3')  
  
2bbv mmCIF Assemblies | 1| complete icosahedral assembly | 2| icosahedral
asymmetric unit | 3| icosahedral pentamer | 4| icosahedral 23 hexamer | 5|
icosahedral asymmetric unit, std point frame | 6| crystal asymmetric unit,
crystal frame  

2bbv citation:    Wery, J.P., Reddy, V.S., Hosur, M.V., Johnson, J.E. (1994).
The refined three-dimensional structure of an insect virus at 2.8 A
resolution. J.Mol.Biol., 235, 565-586. PMID: 8289282. DOI:
10.1006/jmbi.1994.1014  
Opened mmCIF data containing 7817 atoms and 7813 bonds  

lighting full

didn't expected commands hrefs to be to tools/sequenceviewer.html on line 239  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 63008, resource id:
50332189, major code: 40 (TranslateCoords), minor code: 0  

open /home/lab311/Downloads/pdb4wjg.ent

Unrecognized file suffix '.ent'  

Unrecognized file suffix '.ent'  




OpenGL version: 3.3.0 NVIDIA 390.48
OpenGL renderer: Quadro 2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 7 years ago

Component: UnassignedDocumentation
Milestone: 1.0
Owner: set to Greg Couch
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionApparently bogus help viewer error

I can't find any file in the entire source tree where "tools/sequenceviewer.html" is used in a cxcmd href. Also, the error message itself is grammatically incorrect.

comment:2 by Greg Couch, 7 years ago

Resolution: fixed
Status: assignedclosed

Identified as developer debug message in log.

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