User: Jose Manuel Duarte
Jose Manuel Duarte • 280
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Posts by Jose Manuel Duarte
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... As Pierre says it is an issue with a missing dependency in your class path (log4j 2). You can get the jar manually and then point your eclipse project to it. However it is a lot easier and much more powerful to use maven to deal with the dependencies automatically.
BioJava is all set up already to ...
written 3.4 years ago by
Jose Manuel Duarte • 280
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... In order to know whether a particular biounit comes from authors or PISA, you will need to look into the original PDB/mmCIF file. The biounit file only contains the result of applying the symmetry operators present in the REMARK 350 section (or the _pdbx_struct_oper_list field in mmCIF files) and do ...
written 3.8 years ago by
Jose Manuel Duarte • 280
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... There's 2 main reasons for having multiple biounits in the PDB:
When there are multiple equivalent copies of the biounit in the crystal, then they are annotated as several biounits. A very typical example would be 4re6: a dimeric protein with 4 chains in the asymmetric unit. In that example bioun ...
written 3.8 years ago by
Jose Manuel Duarte • 280
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Answer:
A: Bio-Javascript?
... The BioJS project exists for quite some time now and aims mainly at visualisation of biological data. It has already quite a few components, like MSA viewer, tree viewer or protein feature viewer. I don't know the details but I suppose they must have developed a few common data structures, so I woul ...
written 3.8 years ago by
Jose Manuel Duarte • 280
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... I would like to add that PDB files might look simple and thus it is tempting to write your own little parser like that above. In reality there are many subtle issues in the parsing that are best left to mature libraries to handle. Thus I'd recommend the use of Biojava too, see the tutorial
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written 3.8 years ago by
Jose Manuel Duarte • 280
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... You can do it programatically by using Biojava (from version 4). See for instance the tutorial or the demo.
You will be able to do it with either PDB or mmCIF files as input. Thus it will work for even very large molecules. Note that since December 2014 the PDB has transitioned to mmCIF as the main ...
written 3.8 years ago by
Jose Manuel Duarte • 280
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... Impact Factors are hugely over-rated and it is widely acknowledged that they are a deeply flawed concept. They simply tell you what the average impact of other papers published in that journal is. That does not affect the quality or impact of your paper whatsoever.
In my opinion the only thing you ...
written 4.0 years ago by
Jose Manuel Duarte • 280
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... Nope, 4.0 is not released yet. So you either wait until the release or get the sources from github which then will allow you to build locally 4.0.0-SNAPSHOT. Then you can use 4.0.0-SNAPSHOT in your pom
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written 4.0 years ago by
Jose Manuel Duarte • 280
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... I've tried now with Java 8 and I can reproduce the problem when using BioJava 3.1. However using the current BioJava 4.0.0-SNAPSHOT seems to work fine.
...
written 4.0 years ago by
Jose Manuel Duarte • 280
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... Actually I've just seen this in the mailing list: http://mailman.open-bio.org/pipermail/biojava-l/2014-November/011339.html which looks very much like your error and then explains everything: the problem is with Java 8 (I tried with Java 7)
...
written 4.0 years ago by
Jose Manuel Duarte • 280
Latest awards to Jose Manuel Duarte
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: The reason of multiple biounit files for one PDB
Supporter
3.8 years ago,
voted at least 25 times.
Teacher
4.1 years ago,
created an answer with at least 3 up-votes.
For A: Blastclust Has Been Depreciated. Does Anyone Know Why?
Teacher
4.1 years ago,
created an answer with at least 3 up-votes.
For A: Bioinformatics Journal with no publishing fees?
Teacher
4.3 years ago,
created an answer with at least 3 up-votes.
For A: Blastclust Has Been Depreciated. Does Anyone Know Why?
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