[Chimera-users] Extracting masked map region using selected sop piece?

Oliver Clarke olibclarke at gmail.com
Thu Apr 9 11:48:15 PDT 2015

Thanks Elaine, the combination of mask with a selected piece generated by sop split works perfectly, thank you! I read the documentation for vop, sop and volume, but somehow I didn’t come across mask - thanks heaps for your help. This is a very useful feature.


> On Apr 9, 2015, at 2:02 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Oliver,
> Our density-map expert is away from work for a few days, so you may have to wait for more a more learned answer to your various questions.
> I will try to explain what I can.  A volume “region” is a rectangular box, specified by grid indices or by manually drawing a box outline.  It is not defined by isosurface displays of that map.  I call them “subregions” here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#region>
> …and here are the related volume command options:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions>
> Instead, you probably want to use the “mask” command:
> The “sop” command works on surface models.  It does not split the map, just the contour surface so you can separately select disconnected parts of the surface. Although the resulting surface pieces are still part of a single model, after “sop split” you can then select just the part of interest and then use the “mask” command with “sel” as the surface specifier. 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
> Another idea (probably not as good) is to surround that part of the isosurface with the Volume Eraser bubble and use the shortcut eo (or command “ac eo”) to erase outside the bubble, but the result would be spherical instead of shaped like the surface. 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>
> I hope this helps,
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Apr 9, 2015, at 7:44 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> Hi all,
>> I find the sop command (particularly 'sop split' and 'sop hideDust metric volume rank') to be very useful for viewing a molecular envelope at a low threshold in an otherwise noisy map.
>> I would like to save the volume enclosed by a single sop piece as a separate volume, but it does not seem like this is possible - when I select a sop piece and use 'volume nameregion’ to assign it a name, and then attempt to write just that region to an mrc, it saves the whole map. Is there some way to do this that I am missing?
>> I realize that a similar outcome can be achieved with segger, but for larger maps this can be very slow (and potentially involve multiple cycles of selection and regrouping), whereas sop operations are almost instantaneous, so I feel it would be a valuable adjunct capability to that offered by segger.
>> Also, the behaviour of sop split seems a little counterintuitive to me. When I use 'sop split' on a volume, it generates a new model with a different ID for the split map - fine so far. However, the original map seems to be completely invisible - it is listed as displayed in the model panel, but if I undisplay the split map in the model panel and toggle display of the original map in the model panel, nothing happens. If I go to the volume viewer, the original map is listed as displayed, and if I toggle it off and then on again there, it reappears. It seems like it would be maybe simpler for the user to just automatically undisplay the original map upon creation of the sop split map, but not to prevent the user from redisplaying it in the model panel. Here is a link to a screen recording demonstrating what I mean: https://www.dropbox.com/s/g40u9dhj0xslcbf/sop_split.mov?dl=0
>> Best,
>> Oliver.

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