Christoph wrote: > Dear Jmol developers, > > I have tried out Jmol and am impressed by its rendering speed. > > Therefore I have embedded it into the alignment application STRAP.
Excellent! > STRAP is found at > http://www.charite.de/bioinf/strap/ > or in the list of recommended software of the pdb-database. > > STRAP and Jmol already work together reasonably well. > > Joining Strap and Jmol offers many new possibilities: > > One can select residues according to sequence and alignment features. > These selections are shown in Jmol three-dimensionally. > Example: > o intron-exon boundaries, > o sites of high and low sequence conservation, > o mutations, SNPs. > o Prosite patterns > Thus Strap is a bridge for Jmol to alignments and nucleotide sequences. Since I am not a chemist I do not understand the details ... but it sounds great :-) > Since both are written in Java I could think of an even closer > integration. > > I consider to improve some details of the Strap-Jmol communication: > [snip - Several problems identified] It looks like you have been working with the older version of the Jmol source code. I believe that all of these problems have been corrected in the Jmol v10 development version. In addition, you will find that the v10 version is substantially faster when working with macromolecules. > o Should I create a new Jmol instance for each protein ? > > o Can one draw two proteins in one view ? > > o How do I notice when an object is picked ? > > o I did not find out how to rotate in the screen pane (around the > y-axis). > > o can it draw ribbons ? We should get you upgraded to working with the v10 code. Then we can address these issues. We will keep talking. Miguel ------------------------------------------------------- This SF.Net email is sponsored by Sleepycat Software Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver higher performing products faster, at low TCO. http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
