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

Tom Goddard goddard at sonic.net
Mon Apr 13 14:38:42 PDT 2015


Hi Oliver,

  If you use “sop split” to split a map surface into connected components then the mask command can give you the density in one selected surface component as Elaine explained.  You probably want to use the mask “extend” option to include additional grid points outside the surface, otherwise the masked map values will abruptly drop to zero and create a bad looking surface even at the same threshold you used for the original splitting.

  The "sop split” command knows nothing about density maps — it only knows about surfaces.  When it splits a surface it hides the unsplit surface, and the density map code doesn’t realize that happened.  That is why you have some trouble getting it to redisplay the original map — you have to hide and show it in volume viewer, or change threshold.  It shouldn’t work this way.  The technical reason is that Model Panel and Volume Viewer are only paying attention to whether the whole surface model is displayed, and “sop split” does not hide the whole surface model — it only hides the piece it split (which happens to be the entire surface, but in general surfaces can have multiple pieces and some can be hidden and some shown).  Neither Model Panel nor Volume Viewer handle the possibility that a single piece of a surface was undisplayed.  Maybe “sop split” shouldn’t hide the original surface.  But that would lead to confusion.  I’ll file a bug report to someday figure out a better way to handle this.

	Tom


> On Apr 9, 2015, at 11:48 AM, Oliver Clarke wrote:
> 
> 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.
> 
> Oliver.
> 
> 
>> On Apr 9, 2015, at 2:02 PM, Elaine Meng  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 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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