At 8/13/08, Shaun Lott wrote: >One of the limitations I see for my more advanced labs is the lack of a >facility in Jmol to perform overlays of structures, though I appreciate for >displaying single structures, it is indeed pretty comprehensive.
Dear Shaun, Jmol does not do structural alignments. It has nothing equivalent to DeepView (DV)'s fantastic "Fit" capabilities. I myself use DV when I need to do structural alignments. However, Jmol can load: - More than one PDB file (and move them independently) - A single PDB file containing more than one model (using MODEL #/ENDMDL records) - A single model and, using REMARK 350 symmetry operations in the header, display the biological unit (including virus capsids). - Maybe some other possibilities I don't know about? (jmol-users please chime in ...) So, if you align two models in DV and then load them into Jmol, there are many options for displaying them, including independent display, independent rotation etc. Multiple models can also be animated (like a movie) very easily with just a few commands. Proteopedia's Scene Authoring Tool (SAT) has an option to animate models. See for example the page on Morphs for examples of such animations. I am not experienced using the multiple-PDB file loading, but if you'll tell me more specifically what you have in mind, I'll help you figure out how to do it. Bear in mind that, in order to keep it easy to use, the Scene Authoring Tool (SAT) in Proteopedia is meant to handle only the most commonly needed features of Jmol. But, while using the SAT, you can always open Jmol's console and use commands, then use the SAT's save scene (state) to attach the result to a green link. -Eric ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
