Re: [Open Babel] Help to conversion format cif_to_pdb
On 04/14/2014 08:51 AM, David Hall wrote: Can you explain what parts of the file are not compatible that you are looking at? Residue numbering? Temperature Factors? Testing briefly, it appears the coordinates agree, so knowing that fields you are looking to preserve would be useful. SEQRES, temperature factors, the whole header from TITLE to MTRIX... The diff is almost 7MB, I don't think you want to look. IMO even half-way complete conversion is way beyond OpenBabel's job description so I wouldn't bother wasting any time on it. Extracting OBMol from PDB entry is probably hard enough (e.g. what do you do with NMR structure with 50 models and REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 19,23,42). -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Help to conversion format cif_to_pdb
Sorry but i don't understand your answer What's OBMol and what can it do ? in fact babel in openbabel don't translate the file completely it's omits a lot of information. I don't worried about this The point is how different and reliable it is 2014-04-15 14:14 GMT-03:00 Dimitri Maziuk dmaz...@bmrb.wisc.edu: On 04/14/2014 08:51 AM, David Hall wrote: Can you explain what parts of the file are not compatible that you are looking at? Residue numbering? Temperature Factors? Testing briefly, it appears the coordinates agree, so knowing that fields you are looking to preserve would be useful. SEQRES, temperature factors, the whole header from TITLE to MTRIX... The diff is almost 7MB, I don't think you want to look. IMO even half-way complete conversion is way beyond OpenBabel's job description so I wouldn't bother wasting any time on it. Extracting OBMol from PDB entry is probably hard enough (e.g. what do you do with NMR structure with 50 models and REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 19,23,42). -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Obrigado, Wellison Gonçalves -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Help to conversion format cif_to_pdb
On 04/15/2014 03:59 PM, Wellisson Gonçalves wrote: Sorry but i don't understand your answer OpenBabel deals with molecules. PDB deals with studies of crystal structures, extended (with varying degree of success) to structures obtained from EM, NMR, and other methods. The study includes much more than molecule: there's citations, secondary structure, NMR models, sample details and so on and so forth. Dep. on your definition of molecule, it can include more than one. Etc. I don't believe you can reasonably expect OpenBabel to convert all of that information between 2 PDB formats: it's not what it's for. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Help to conversion format cif_to_pdb
Ok Thanks for the interest Now, i need to convert the format, only and it's necessary that it has the best fidelity possible with the original structure I think it's openbabel can't help me I'm going to research more 2014-04-15 19:09 GMT-03:00 Dimitri Maziuk dmaz...@bmrb.wisc.edu: On 04/15/2014 03:59 PM, Wellisson Gonçalves wrote: Sorry but i don't understand your answer OpenBabel deals with molecules. PDB deals with studies of crystal structures, extended (with varying degree of success) to structures obtained from EM, NMR, and other methods. The study includes much more than molecule: there's citations, secondary structure, NMR models, sample details and so on and so forth. Dep. on your definition of molecule, it can include more than one. Etc. I don't believe you can reasonably expect OpenBabel to convert all of that information between 2 PDB formats: it's not what it's for. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu -- Obrigado, Wellison Gonçalves -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Help to conversion format cif_to_pdb
I know about that But i don't get compile I receive a lot of compilation errors But a find a other tool http://sw-tools.pdb.org/apps/CIFTr/index.html It's very simple But i'm developing a bioinformatics tool using C++ with QT for platforms linux, MAC OS X and windows It's necessary to me put a function that convert .cif to .pdb I'm already using openbabel for other functions. And I would very much like to use it to babel I have no idea how to integrate http://sw-tools.pdb.org/apps/CIFTr/index.html or http://sw-tools.rcsb.org/apps/MAXIT/index.html in my aplication. They are using a lot of directories in the project. Thanks Wellisson 2014-04-13 12:55 GMT-03:00 Dimitri Maziuk dmaz...@bmrb.wisc.edu: On 4/12/2014 2:20 PM, Wellisson Gonçalves wrote: A use the executable babel with parameters babel -icif '4POQ.cif' -opdb '4POQ_cif_to_pdb.pdb' And i received the file that not compatible with the original file. I know becouse i downloaded the original file in website 4POQ.pdb and It's different I doubt OB can deal with a complete pdb file -- either pdb or mmcif. Try http://sw-tools.rcsb.org/apps/MAXIT/index.html Dimitri -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Obrigado, Wellison Gonçalves -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Help to conversion format cif_to_pdb
On 4/12/2014 2:20 PM, Wellisson Gonçalves wrote: A use the executable babel with parameters babel -icif '4POQ.cif' -opdb '4POQ_cif_to_pdb.pdb' And i received the file that not compatible with the original file. I know becouse i downloaded the original file in website 4POQ.pdb and It's different I doubt OB can deal with a complete pdb file -- either pdb or mmcif. Try http://sw-tools.rcsb.org/apps/MAXIT/index.html Dimitri -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
