On Thu, Aug 6, 2015 at 7:12 AM, Rolf Huehne <rhue...@fli-leibniz.de> wrote:
> 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.) > I am not ready to jump for this. What code is producing this file? I'm guessing you are usurping the mmCIF format for your own purposes, right? I think it is very clever to use _atom_site.auth_seq_id for these purposes, and we could consider that, though it cannot be a default to read this data block, since it is not the same as CONECT, and it is not consistent with Jmol's standard autobonding business. > > --- 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). > 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. > > 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} > > That's a bug due to the longer-than-three-character residue names. (fixed, or at least those are truncated to 3 char) > 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. > Suggestions: > A) It would be nice if the atoms could transfer their current color to > the atoms in the plot. > that is the case -- now that it is fixed (sort of) for residue names. > > 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. > > 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 > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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