On 10/07/2014 04:50 PM, Angel Herráez wrote: > Hi Rolf > > This is interesting but not what I can really discuss about, but I'd > contribute one or two hints: > > One really nice thing (I've seen it in other tree viewers) would be > the ability for the user to pull a node and have the whole thing > rearrange dynamically. That's a force field and Jmol already does > this with dragMinimze. > However, probably not easy to achieve seeing the complexity of your > trees (i.e. many "bonds" tied to an "atom"). > Yes, Angel. It would be one of the next steps to make the layout directly editable by the user. It could be completely manually or manually-directed like you describe it. But for this you need a reasonable initial layout. I will keep this in mind if I ever get past the first step.
>> Q: Does JSmol allow that an atom is part of more than one residue or >> would this interfere with something? > > Quick answer: no atom can belong to 2 residues. > > But I would forget about "residues". I'd just define Jmol variables > as atom sets and assign each node to as many of them as you wish > (using a script). > It is as easy to select by user variables / atomsets as by residue. > Another possibility is to assign custom atom properties, instead of > atom sets. > That is what I do within the 'Jena3D Viewer' for the different mappings (SAPs/SNPs, PROSITE motifs etc.). And from there I know that commands can be very slowly this way. Handling for example several hundred SNPs by using sets already takes quite some time (see for example http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1A00&APPLET=HTML5). And in the network viewer the number of sets would potentially be much higher. It will also require to rebuild a lot of built-in functions to get similar (slower) functionalities. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
