Sorry, I should have explained what that is doing. When a PDB file has alternate locations, it indicates (usually) that two models are being delivered as one. Most of the coordinates, for whatever reason, are considered common to both models, but some are different. Typically, these are different conformations of the same atoms, thus the idea of "alternate" (or what I would have said, "alternative") locations.
When a protein in particular has alternate locations for its atoms, an interesting situation arises. What is a helix in one conformation may not be a helix in another. To treat this situation properly, a visualizer basically has to create two completely independent models, calculate the protein structure, and display the two independently. Earlier Jmol versions ignored this. Jmol 11 introduces the "configuration" command to deal with alternate location data. The command may not do anything obvious, but it serves two functions. First, it acts as a select command, selecting all atoms in a model for which no alternate location data is provided (the atoms common to all models). Second, it reruns the structure calculation to allow the cartoons to reflect the changed conformation. In reality, the "configuration" command is simply a convenience. So, for example, configuration 1 selects for the first embedded model, and configuration 2 selects for the second. Why not just use select, you say? Well, it turns out that authors can use just about any character they want to designate alternate locations. A and B, Q and Z, 1 and 2, etc. The authors of 2tbv, for example, used P and S. The authors of 5hvp used 1 and 2. The authors of 1zir used ABCDEFGHIJKLMNOPQRSTUV. Without detailed knowledge of a particular author's choice, we cannot just generally select for these using the "select" command. So, in one case configuration 1 is roughly equivalent to select *% or *%A calculate structure and in another it is roughly select *% or *%1 calculate structure This isn't an exact equivalence, because the "calculate structure" command clears all secondary structure, but "configuration 1" does not. Right now I can't remember how that bit of magic works. So, mostly, the configuration command, is just a convenience. It's real power comes in situations where we might have, say, a database and Jmol is being used as a general viewer. Jmol catalogs the configurations numerically, regardless of author notation. "configuration 1" is always the first alternative, "configuration 2" is the second, etc. There are situations where it still fails, I think, and one simply has to go back to hand coding select, but those are very few. For example, 1phb uses AB12, probably to indicate that A/B and 1/2 are independent -- that the real configuration is A1, B1, A2, B2. Right now Jmol doesn't attempt to show this sort of mix-and-match properly. Best in that case is to use select *% or *%A or *%1 Bob configuration 1 David Leader wrote: >Angel wrote: > > > >>>As regards the bad display, select single motif display and then >>>Catmat: 48,48,50 . Glu 50 is screwed up. >>> >>> >>> >>That looks that an alternate position (Alt) problem; there are e.g. >>[Glu]50:A.CD%A and [Glu]50:A.CD%B, and Jmol is drawing both. >>I have not used Alt locations, but I know it's been dealt with; >>make sure to >>read the doc for that. >> >>Yes! Using the pop-up menu: "Configurations", you have A, B and C; >>check >>"A" and your funny Glu is gone. >> >> > >Ah, that's the problem. But although I confirm that selecting >Configuration A from the pop-up does the trick I cannot for the life >of me get it to work as a script, either in the console or on the >page. I checked > >http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/ >altloc.htm > >but "conformation A" does nothing for me. It seems to be 'taking' in >the script, because if I load the page that way, I no longer have >conformation options on the menu. Any idea what I'm doing wrong? The >script was of the type: > >jmolRadio("echo; restrict (81,82,83) AND protein AND NOT >(*.H,*.H?,*.H??, *.H???, *.?H, *.?H?, *.?H??, *.?H???); centre >selected; wireframe 0.3; zoom 5000; select [CU], [ZN]; spacefill; ", >"", ""); > >and I've tried 'conformation A' just anywhere it could go. > >Regarding the jmolSetCheckboxGroup A, Angel replied to my comment: > > > >>>As regards the jmol.js bug, check All Motifs and then uncheck any of >>>the ones below. All remains checked. >>> >>> >>> >>That is so by design, David; quoting the doc: >>"Whenever one of the followers is checked or unchecked, its >>siblings are >>examined; if all have the same state, the leader will be checked or >>unchecked accordingly." >> >>I know that's debatable, but since there is no "grey" state for a >>checkbox, >>one choice or the other must be taken. Bob took this. If you >>uncheck all >>siblings individually, the master wll automatically unckeck. >> >> > >I think the decision was wrong. I would - it was not the one in my >original Master/Slave implementation. If all checkboxes are not >checked, then it seems to me illogical for the 'leader' - entitled >'All' to be checked. It also seems inconsistent with the rest of the >behaviour. >However, I can always restore my Master/Slave version to the latest >version of Jmol.js, or perhaps give up using JmolCheckboxes for >JmolScript (only just discovered it - needed if you want to drive >several scripts from one button) and drive it from my own >external .js file, which would be easier to maintain. > >Thanks again for everyone's forbearance. > >David > > > > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. 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