Angel Herraez wrote: > >1) We have "select */2", "display /*2", "model 2" and "frame 2" >On a single multi-model PDB file: do they refer to the second model or to >model named "2" ? > > For PDB files, "2" refers to the second model UNLESS a MODEL record is present, in which case "2" refers to the model with
MODEL 2 in it. >The doc says (or said) that "model 2" refers to model named "2" while "frame >2" refers to >second model. > > I was considering making that change -- I have it commented out in the code because in the end I thought it would not be a wise change. Now that we have the decimal business I think it's just as well if we leave it that way -- frame and model exactly the same command. >On XYZ and other files, there's only the order meaning, of course. > > > > Right. >2) Just for the records: the new capability, "frame 1 5" allows to display >two frames/models, >same as "display */1,*/5" but it is not "two background models", right? An >"anim" will forget >thse two models and start animating, or use the single one specified by "set >backgroundModel" > > > frame 1 5 does nothing, or isn't supposed to, anyway. frame range 1 5 sets the range for animations. If it is a PDB file that contains models, then the range is from whatever model is labeled "1" to whatever model is labeled "5". Otherwise, it's the first through the 5th model for the range. "anim off/play/revplay/pause/resume/rewind" all act within the defined frame range. "frame 0" also acts within the range, showing all models, provided their atoms are also "displayed". "anim" by itself does a full reset of animation; it is short for "animation on"; any frame range set previously is unset. "frame ALL" also resets the range, but it displays all the models as well. Once I get it checked in, frame range all will also reset the frame range to all models while displaying just the first model. display 1.1, 1.5 does exactly that, PROVIDED models 1.1 and 1.5 are within the defined frame range, and all models are "turned on" with frame 0 The trouble is that there are two commands with similar effects. frame x.x frame range x.x y.y frame 0 frame all are the commands that determine what models are active and CAN be "displayed" frame x.x # sets one model to be active; display * will display only this model frame range x.x y.y #sets a range of models to be active for animation; display * will display only the first model frame 0 # allows display * to display all atoms in all models in the specified range frame all # resets the range; allows display * to display all atoms in all models At all times there is a certain "display set" of atoms. These frame commands do not have any effect on that set. Initially, and in earlier versions of Jmol, we only had, effectively, "display *", so this wasn't an issue. With the addition of "display", now we have two layers of control on what atoms and models are displayed. I think of "display" as atom-based and "frame" as model-based. But because we can select for models, as with "display 1.2", it gets a bit tricky. Bob ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
