Re: [Biojava-l] 3D viewing?

Hi Egon! I am the person who contributed the biojava - structure classes. As it turns out I am a very happy Jmol user already for quite a while now! :-) Using both Biojava and Jmol I am working on a 3D - DAS (distributed annotation system) client to visualize annotations of proteins in both s

Re: [Biojava-l] 3D viewing?

Andreas Prlic wrote: Hi Egon! I am the person who contributed the biojava - structure classes. As it turns out I am a very happy Jmol user already for quite a while now! :-) Seconded - Jmol is very cool and surprisingly easy to integrate if you have PDB format data lying around somewhere in your

Re: [Biojava-l] 3D viewing?

On Tuesday 11 January 2005 11:49 am, Tom Oinn wrote: > Andreas Prlic wrote: > > I am the person who contributed the biojava - structure classes. As it > > turns out I am a very happy Jmol user already for quite a while now! :-) > > Seconded - Jmol is very cool and surprisingly easy to integrate if

[Biojava-l] Biojava DB

Hello, I am thinking of using BioJava for managing sequences and annotations of sequences. BioJava seems to have database support for storing sequences in relational databases. How developed is the support for storing annotated sequences? Is there any documentation (other than JavaDoc) on working

Re: [Biojava-l] 3D viewing?

Egon Willighagen wrote: On Tuesday 11 January 2005 11:49 am, Tom Oinn wrote: Andreas Prlic wrote: I am the person who contributed the biojava - structure classes. As it turns out I am a very happy Jmol user already for quite a while now! :-) Seconded - Jmol is very cool and surprisingly easy to in

Re: [Biojava-l] 3D viewing?

On Tuesday 11 January 2005 01:17 pm, Tom Oinn wrote: > Having a relatively standard intermediate representation such as PDB > format flatfiles is generally a good thing and makes it easier to link > components in a loosely coupled fashion at the expense potentially of > some efficiency. My thoughts

Re: [Biojava-l] 3D viewing?

Hi Egon! What would be the advantages of using a BioJavaModel Adapter ? * faster loading of structure into Jmol ? * fewer memory consumption of application ? * if you rotate the structure in Jmol, the rotated coordinates are available through the biojava structure object ? how about performance

Re: [Biojava-l] 3D viewing?

On Tuesday 11 January 2005 02:03 pm, Andreas Prlic wrote: > Hi Egon! > > What would be the advantages of using a BioJavaModel Adapter ? > > * faster loading of structure into Jmol ? > * fewer memory consumption of application ? Yes, I think so, because one does not need to make a large String firs

[Biojava-l] SequencePanel changes between 1.3 and 1.4pre1

I've just started looking at 1.4pre1 (sorry to take so long!). I am using SequencePanel's to view protein sequences. I add multiple SequencePanels (each having the same sequence) to a Container with a BoxLayout. Each displays a different RangeLocation with the overall effect that the sequence appe

[Biojava-l] biosql support in bioperl?

I'm afraid to ask this on the bioperl list for fear of getting flamed, but I was always under the assumption that bioperl could read and write from a biosql schema, like I have been doing with biojava for some time. The bioperl HOWTO docs read Important Support for the biosql protocol is disabl

Re: [Biojava-l] Biojava DB

Hi - You would probably want to use something like BioSQL. There is some documentation under the OBDA section of this page http://www.biojava.org/docs/bj_in_anger/index.htm There are some people on the list who are actively working with this. You would probably aslo want to look at the BioSQL