[Chimera-users] vop scale and vop morph (maybe chimeraX?)

Tom Goddard goddard at sonic.net
Thu May 11 17:57:26 PDT 2017

Hi Oli,

  I could see that being useful.  Currently the “vop morph” command in Chimera and “volume morph” command in ChimeraX take a scaleFactors option that lets you set scale factor for each of the maps in the morph.  But I agree it is a pain to set those scale factors.  The “vop subtract” and “volume subtract” commands also have a scaleFactors option but in addition has a “minRMS true/false” option that automatically scales all but the first map so that the sum of the squares of the difference of the scaled map with the first map is minimized.  It would be nice to have this minRMS option in the morph command, and it would be pretty easy since there is already code to do it for subtract.

  I expect I’ll only add this to ChimeraX since all new features are going into only ChimeraX since we don’t have enough people to add every feature to Chimera and ChimeraX.  I’ve made a ticket for this improvement.

	http://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/667 <http://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/667>

I don’t think it is a high priority compared to a hundred other enhancements in the queue but eventually I will get to it.  Thanks for the suggestion.


> On May 11, 2017, at 11:11 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> Hi,
> When I morph two maps, if they have different mean/sd, I always have to scale the mean and sd of the second map to that of the first, otherwise the morph looks very non-linear - nothing happens until fraction 0.9, and then the morphing happens increasingly fast (so not ideal for visualization).
> If I normalize one map to the other I get a beautiful, smooth, linear morph.
> Would it be possible in either chimera or chimeraX to automate this? Either to add an option to vop scale to scale one map directly to the parameters of another (rather than having to use vop measure mapstats) or to have an option for vop morph to put both maps on the same scale?
> Cheers
> Oli
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