part II of that... See http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.15_2015.08.08.zip
Also releasing that on SourceForge. On Fri, Aug 7, 2015 at 6:09 AM, Rolf Huehne <rhue...@fli-leibniz.de> wrote: > >> > >> Oddities: > >> 1) Negative temperature values are plotted as zero (e.g.: atom 17). > >> > > > > it's not that it is zero, only that it is on the axis. Hover over it, and > > you will see that it has the proper value. > > > It is quite unexpected that the axis doesn't indicate zero, especially > if there is no label indicating the non-standard value. > I suppose. They are meant only to be references. You can remove the x-axis with draw plotaxisx? delete > > > >> 3) Residue names with more than three letters are truncated in the plot > >> to three letters, e.g.: "OB_INC" -> "OB_" > >> > >> This format cannot support long names. > > > Q: Does 'this format' mean 'plot format' or something else? > I tested if Jmol could handle residue names with six characters and I > didn't observe any problems, for example with selection commands or labels. > Only this plot issue. It was just that the Jmol plot format uses PDB format, and it was messing up with that multi-character name. I have found a work-around for that, and it is now working properly. So there is no limitation on atom name or residue name now. > > > > > > > >> Suggestions: > >> B) In extension to A) it would be nice if also other atom properties > >> would be transferred, but at least those that are plotted. Then for > >> example a 'hover' like the one defined in the example above would show > >> the same in the plot and the model frame. And one could look up the > >> exact values of the plotted properties. > >> > > > > Can't have it both ways, unfortunately. > > > I am not sure what 'both ways' means here. Maybe I wasn't clear enough. > I just wanted that properties are transferred from the model to the plot > while it is created. Afterwards properties might differ because of user > interactions. > Yes, I see. I have added that feature. In the case of the plot parameters being x, y, or z, then those are preserved as property_x, property_y, and property_z instead of reinstated as actual x,y,z coordinates. This is because the PLOT command scales data automatically, setting x,y,z from that scaling. Other parameters are preserved as long as they are settable. Bob
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