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. 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 both are written in Java I could think of an even closer integration. I consider to improve some details of the Strap-Jmol communication: The residue selection does currently not respect the chain identifier. When one selects for example residues 20-29 in a protein which has two chains residues 20-29 of chain A as well as of chain B are highlighted even when I want to select only in chain A. I do not completely understand the select-command of Jmol. I experienced that the select command has no effect when sent via Jmol.control.evalString(String) even though the same command works at the script shell window. Therefore I chose a different method: BitSet Jmol.control.getEval().getResidueSet(from, to); and Jmol.control.addSelection(BitSet);; Since from and to are integer numbers I do not know how to encode the chain id. There are some tiny problems: o Strap is an alignment program and therefore selects entire amino acids. Applying the label command adds labels to each atom which I do not want. Is there something like "label_residue". 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 ? I would be glad when you could have a look at it. The source text of the Jmol2strap class can be viewed by pressing the java-icon. I already placed a link to your Jmol site on the web-site of Strap. Could you add a link to Strap on your site ? Best regards Christoph ------------------------------------------------------- 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
