| Summary: | Unable to load a molecule in molecular editor | ||
|---|---|---|---|
| Product: | [Applications] kalzium | Reporter: | Linuxcomics <linuxcomics> |
| Component: | general | Assignee: | Kalzium Developers <kalzium> |
| Status: | RESOLVED WORKSFORME | ||
| Severity: | normal | CC: | annma, marcus |
| Priority: | NOR | Keywords: | investigated, triaged |
| Version: | unspecified | ||
| Target Milestone: | --- | ||
| Platform: | unspecified | ||
| OS: | Linux | ||
| Latest Commit: | Version Fixed In: | ||
| Sentry Crash Report: | |||
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Description
Linuxcomics
2009-04-14 15:47:02 UTC
It sounds like openbabel is broken and not able to find its format plugins. Have you tried testing the babel program too? Kalzium uses the Avogadro library, which uses OpenBabel to load and save molecules. Excuse me but what do you mean by "testing the babel program too" ? Update installed version of OpenBabel by compiling the last stable release ? Open Babel comes with some command line programs that also use the library. The babel program is one such program - translate from one file format to another. You could try `babel -H` and see what file formats are listed. Also taking one chemical file and translating it to another. So the Avogadro tarball has several test files - try `babel methanol.cml methanol.xyz` for example and confirm the file is successfully translated. LinuxComic, can you do what Marcus explained please? Thanks in advance. (In reply to comment #4) > LinuxComic, can you do what Marcus explained please? Thanks in advance. Sorry, I was very busy last days. I will try to do the tests tomorrow. Best regards, Linuxcomics. When I use the command 'babel -H', there is a message which says : "The following file formats are recognized: acr -- ACR format [Read-only] adf -- ADF cartesian input format [Write-only] adfout -- ADF output format [Read-only] alc -- Alchemy format arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] bgf -- MSI BGF format box -- Dock 3.5 Box format bs -- Ball and Stick format c3d1 -- Chem3D Cartesian 1 format c3d2 -- Chem3D Cartesian 2 format cac -- CAChe MolStruct format [Write-only] caccrt -- Cacao Cartesian format cache -- CAChe MolStruct format [Write-only] cacint -- Cacao Internal format [Write-only] can -- Canonical SMILES format. car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] ccc -- CCC format [Read-only] cdx -- ChemDraw binary format [Read-only] cdxml -- ChemDraw CDXML format cht -- Chemtool format [Write-only] cif -- Crystallographic Information File ck -- ChemKin format cml -- Chemical Markup Language cmlr -- CML Reaction format com -- Gaussian 98/03 Input [Write-only] copy -- Copies raw text [Write-only] crk2d -- Chemical Resource Kit diagram(2D) crk3d -- Chemical Resource Kit 3D format csr -- Accelrys/MSI Quanta CSR format [Write-only] cssr -- CSD CSSR format [Write-only] ct -- ChemDraw Connection Table format cub -- Gaussian cube format cube -- Gaussian cube format dat -- Generic Output file format [Read-only] dmol -- DMol3 coordinates format dx -- OpenDX cube format for APBS ent -- Protein Data Bank format fa -- FASTA format [Write-only] fasta -- FASTA format [Write-only] fch -- Gaussian formatted checkpoint file format [Read-only] fchk -- Gaussian formatted checkpoint file format [Read-only] fck -- Gaussian formatted checkpoint file format [Read-only] feat -- Feature format fh -- Fenske-Hall Z-Matrix format [Write-only] fix -- SMILES FIX format [Write-only] fpt -- Fingerprint format [Write-only] fract -- Free Form Fractional format fs -- FastSearching fsa -- FASTA format [Write-only] g03 -- Gaussian98/03 Output [Read-only] g92 -- Gaussian98/03 Output [Read-only] g94 -- Gaussian98/03 Output [Read-only] g98 -- Gaussian98/03 Output [Read-only] gal -- Gaussian98/03 Output [Read-only] gam -- GAMESS Output [Read-only] gamess -- GAMESS Output [Read-only] gamin -- GAMESS Input gamout -- GAMESS Output [Read-only] gau -- Gaussian 98/03 Input [Write-only] gjc -- Gaussian 98/03 Input [Write-only] gjf -- Gaussian 98/03 Input [Write-only] gpr -- Ghemical format gr96 -- GROMOS96 format [Write-only] gukin -- GAMESS-UK Input gukout -- GAMESS-UK Output gzmat -- Gaussian Z-Matrix Input hin -- HyperChem HIN format inchi -- InChI format inp -- GAMESS Input ins -- ShelX format [Read-only] jin -- Jaguar input format [Write-only] jout -- Jaguar output format [Read-only] k -- Compare molecules using InChI [Write-only] log -- Generic Output file format [Read-only] mcdl -- MCDL format mcif -- Macromolecular Crystallographic Information mdl -- MDL MOL format ml2 -- Sybyl Mol2 format mmcif -- Macromolecular Crystallographic Information mmd -- MacroModel format mmod -- MacroModel format mol -- MDL MOL format mol2 -- Sybyl Mol2 format molden -- Molden input format [Read-only] molreport -- Open Babel molecule report [Write-only] moo -- MOPAC Output format [Read-only] mop -- MOPAC Cartesian format mopcrt -- MOPAC Cartesian format mopin -- MOPAC Internal mopout -- MOPAC Output format [Read-only] mpc -- MOPAC Cartesian format mpd -- Sybyl descriptor format [Write-only] mpqc -- MPQC output format [Read-only] mpqcin -- MPQC simplified input format [Write-only] msi -- Accelrys/MSI Cerius II MSI format [Read-only] msms -- M.F. Sanner's MSMS input format [Write-only] nw -- NWChem input format [Write-only] nwo -- NWChem output format [Read-only] out -- Generic Output file format [Read-only] outmol -- DMol3 coordinates format pc -- PubChem format [Read-only] pcm -- PCModel Format pdb -- Protein Data Bank format png -- PNG files with embedded data pov -- POV-Ray input format [Write-only] pqr -- PQR format pqs -- Parallel Quantum Solutions format prep -- Amber Prep format [Read-only] qcin -- Q-Chem input format [Write-only] qcout -- Q-Chem output format [Read-only] report -- Open Babel report format [Write-only] res -- ShelX format [Read-only] rsmi -- Reaction SMILES format rxn -- MDL RXN format sd -- MDL MOL format sdf -- MDL MOL format smi -- SMILES format smiles -- SMILES format sy2 -- Sybyl Mol2 format t41 -- ADF TAPE41 format [Read-only] tdd -- Thermo format test -- Test format [Write-only] therm -- Thermo format tmol -- TurboMole Coordinate format txt -- Title format txyz -- Tinker MM2 format [Write-only] unixyz -- UniChem XYZ format vmol -- ViewMol format xed -- XED format [Write-only] xml -- General XML format [Read-only] xtc -- XTC format [Read-only] xyz -- XYZ cartesian coordinates format yob -- YASARA.org YOB format zin -- ZINDO input format [Write-only]" When I try `babel methanol.cml methanol.xyz`, the translation fails. "babel methanol.cml methanol.xyz ============================== *** Open Babel Error in OpenAndSetFormat Cannot open methanol.cml 0 molecules converted 1 errors" Bests regards, Linuxcomics. Dear Bug Submitter, This bug has been in NEEDSINFO status with no change for at least 15 days. Please provide the requested information as soon as possible and set the bug status as REPORTED. Due to regular bug tracker maintenance, if the bug is still in NEEDSINFO status with no change in 30 days the bug will be closed as RESOLVED > WORKSFORME due to lack of needed information. For more information about our bug triaging procedures please read the wiki located here: https://community.kde.org/Guidelines_and_HOWTOs/Bug_triaging If you have already provided the requested information, please mark the bug as REPORTED so that the KDE team knows that the bug is ready to be confirmed. Thank you for helping us make KDE software even better for everyone! This bug has been in NEEDSINFO status with no change for at least 30 days. The bug is now closed as RESOLVED > WORKSFORME due to lack of needed information. For more information about our bug triaging procedures please read the wiki located here: https://community.kde.org/Guidelines_and_HOWTOs/Bug_triaging Thank you for helping us make KDE software even better for everyone! |