Hi all, I explored the 'plot PROPERTIES' command in Jmol 14.3.14_2015.06.06 and noticed some odd behaviour and have a few suggestions.
As example an mmCIF format file was loaded, temporarily available at "http://www.fli-leibniz.de/~rhuehne/jmol/plot_example.cif";. The "_struct_conn" bond records are ignored. But I hope this will change soon. (At least Bob admitted some time ago on this list that it should have higher priority with regard to the plans of the PDB to drop PDB format files from their FTP site soon.) --- Example commands --- load "plot_example.cif" hover "[%[group]]:%[atomName] #%[atomno] temp=%[temperature]" plot PROPERTIES atomno temperature ------------------------ Oddities: 1) Negative temperature values are plotted as zero (e.g.: atom 17). 2) Zero temperature values are plotted with a shift in the z-axis (500 instead of -100) and the y-axis (-22.7 instead of -100), e.g. atom 1 and 16: $ print {2.1 and @1}.xyz {-100.0 -22.6938 500.0} $ print {2.1 and @2}.xyz {-92.0 19.6863 -100.0} $ print {2.1 and @3}.xyz {-84.0 15.9963 -100.0} $ print {2.1 and @16}.xyz {20.0 -22.6938 500.0} 3) Residue names with more than three letters are truncated in the plot to three letters, e.g.: "OB_INC" -> "OB_" Suggestions: A) It would be nice if the atoms could transfer their current color to the atoms in the plot. 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. 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: rhue...@fli-leibniz.de 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 ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
