Hi Sara, which version are you using? I can't reproduce that with 12.3.12 and 12.2.12.
With this script everything looks normal: set pdbaddhydrogens ; load=1H6I ; cpk off ; wireframe on ; select [TYR]227:A OR [ALA]232:A ; wireframe 0.15 ; cpk 25% ; center selected ; zoomto 1 (selected) 500; rotate y -70.0 -2 spin ; delay 3 ; selectionhalos on ; select [ALA]232:A ; delay 3 ; select [TYR]227:A ; delay 3 ; select [ALA]232:A.H Oliver On Fri, Mar 9, 2012 at 14:50, Sara Bonner <bonn...@mit.edu> wrote: > HI > > Using the set addPdbHydrogens functionality I am finding that sometimes the > hydrogens are associated with more than one amino acid. Are you making the > hydrogen selection based on the label of the hydrogen or based on its > distance from the surrounding atoms? Is there any way to have control over > this? > > Example: > set addPdbHydrogens; > load=1H6I; > select [ALA]232:A; > spacefill 100%; > select [TYR]227:A; > spacefill 50%; > > Note how the hydrogen atom labeled [ALA]232:A.H #3348 changes in size for > both selections. > > This becomes relevant for me as I am sorting hydrogen bonds according to the > structures they apply to. From the example given about, according to the > label on the hydrogen this should be a tertiary hbond between the oxygen in > 227 and the hydrogen in 232 and that part works fine. The problem comes in > when this same hbond is added to the secondary hbonds. Because both the O > and H atoms are considered to be in the same amino acid bondMode AND doesn't > help. > > Thanks > Sara > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
