[Chimera-users] Save Cluster Figure as Phython Object

Eric Pettersen pett at cgl.ucsf.edu
Tue Jun 9 17:11:10 PDT 2015

Hi Matthias,
	So you want to do more than save a PNG image and adjust that in Photoshop?  If so, that's too bad because the PNG/Photoshop thing is kind of easy.  I've included directions for that at the end of this message just in case.
	I think the only option is to write some Python code to directly manipulate the matplotlib chart in Chimera itself.  Once you've loaded your trajectory and run the clustering, you would find the MD Movie instance as outlined in this previous chimera-users message:


The overall matplotlib Figure is then:  mdm.clusterDialog.mpFigure
The timeline/cluster subplot is mdm.clusterDialog.timeLine

Let me know if you need more help.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

	You can save a PNG image of the chart by clicking on the rightmost icon in the row of icons below the chart (the one that looks like a floppy disk).  You could then adjust the figure further in Photoshop or what not.
	You may want to use the icon just to the left of the floppy-disk icon first.  That will bring up some sliders to adjust the scaling of the figure.  By default Chimera has scaled the figure so that the frame numbers below the chart are "off screen" but the unadjusted PNG will probably show the top half of those numbers, so therefore adjusting the scaling may be desirable.

On Jun 9, 2015, at 5:10 AM, "Beuerle, Matthias" <m.beuerle14 at imperial.ac.uk> wrote:

> Dear all,
> I have been using the Clustering tool in the MD Movie/Analysis/Cluster to examine my trajectories and I found it very useful. Now I would somehow like to save the box-chart matplotlib object in order to adjust the figure, so that I can use it for a publication, since the dialog buttons do not allow a lot of modifications. Is this possible somehow?
> Alternatively I would be very happy as well if one could use the output obtained from the 'Save' button to recreate a similar figure (in which I have failed so far). Help is very much appreciated.
> Kind regards,
> Matthias
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> Chimera-users at cgl.ucsf.edu
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