On 06/19/2014 02:44 PM, [email protected] wrote: > Dear all, > > I've come across a couple of issues displaying 2 pdb files; I expect there > are much easier ways to do what I'm trying to achieve and I'm just making > life difficult for myself! > > The documentation (and this mailing list response: > http://www.bioinformatics.org/pipermail/molvis-list/2007q2/000427.html) > suggest that this should work: > > script: 'load FILES "data/1crn.pdb" "data/2OL9.pdb"' > > but in my case (http://www.ccpem.ac.uk/jsmol_test/test2.html) 1crn does > not get shown e.g. clicking the 'hide 1.1' button does hide 1crn, showing > that 2ol9 is not there. Only if the checkbox is clicked does 2ol9 appear. > > After finding > https://www.mail-archive.com/[email protected]/msg12061.html, > I also tried > > script: 'load "data/1crn.pdb"; load append "data/2OL9.pdb"' > > but this also doesn't work - this only displays 2ol9. > > In short, I want both pdb files to be loaded and displayed, with a > checkbox for each structure that toggles the display of just that structure > (this latter bit I assume will be achieved by using the "display > <n.1>,displayed", etc, notation). > > Any help in pointing out my mistakes will be hugely appreciated. > I just pointed the problem out a few days ago in a similar thread concerning the display of multiple models of biological unit files from the PDB. The same also applies to multiple files.
Quote (corrected): "It wasn't obvious from your question that you already had trouble viewing the whole biological unit. There is another command involved here, the 'frame' command (see http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm#frame) By default only the first model of a file is displayed. You need to run the command 'frame all' to see all models at once. Then you can use the 'display' command to restrict the view. But you must be careful not to loose track which setting was made by both commands. In the following example you will see nothing because the setting of the other command prevents the display of anything: frame 2; display *:A/1; Or in this example you will only see model 2: frame 2; display all If you work with the display/hide commands I would recommend to set always 'frame all' first, unless you know what you are doing and always keep the current 'frame' command setting in mind." 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: [email protected] 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 ------------------------------------------------------------------------------ HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
