[Chimera-users] save colored blobs in session

Tom Goddard goddard at sonic.net
Tue Aug 20 16:13:35 PDT 2013


Hi Zoltan,

  Forgot to mention one neat trick.  If you can split the surface into connected pieces and still have decent rendering speed, you can do fancier coloring, for instance color everything near a given blob.  In the image I attached, the pink blobs are all within 10 Angstroms of the green blob.  I selected them by first selecting the green blob with the mouse (ctrl-click) then using the command "zone sel 10 #1"  (selects all surface pieces of model #1 within 10 Angstroms of the current selection).

	Tom



On Aug 20, 2013, at 4:04 PM, Tom Goddard  wrote:

> Hi Zoltan,
> 
>   Unfortunately sessions don't save colors of a density map contour surface set by the Measure and Color Blobs dialog.  It should.  But here's the technical reason that it doesn't.  With a density map contour surface one commonly changes the contour level and the surface changes shape.  Methods for coloring the surface are responsible for updating the coloring.  Sometimes this is possible, for example if the surface is colored by distance from the center (radial coloring), but other times it is not possible, for instance if you colored connected blobs, those blobs may have merged.  If you change contour level the color blobs coloring simply disappears.  Also the color blobs tool does not save its results in session files.  Currently only coloring methods that know how to recolor a surface save their coloring in a session file.  The reason for that is because the density map surface is not saved in the session file.  It is simply recomputed when the density map is opened.  Know doubt this was more than you wanted to know.
> 
>   Let me suggest another way to do it where the coloring will be saved, and maybe you can even do better color annotation.  Make your density map surface (say model #0), then use command "sop split #0".  This will create a copy of the surface where each connected blob is a separate selectable piece.  You can still use Measure and Color Blobs, or you can simply select a blob with the mouse (ctrl-click) and color it (e.g. Actions / Color / From Editor).  Because you can select any blobs you want you can also hide or show whichever you like (Actions / Surface / Show or Hide.  And any coloring or show/hide state for this model will be saved in the session file.  The reason this one gets its colors saved is because the whole surface is saved in the session file because it is not a density map.  It is simply a surface that was copied from a density map surface.
> 
>   The drawback of this method is that Chimera may get very slow if you split a surface with 100,000 pieces.  If that is your situation (likely for EM tomogram data unless you cut out a small region) then you can instead simply copy the density map surface with a command "sop finerMesh #0 spacing 100".  This copies the surface but does not split it into selectable connected blobs.  So then you will have to use Measure and Color Blobs to color individual blobs as you are doing now.  This finer mesh command actually will not make a finer mesh if you choose the mesh spacing bigger than your density map grid spacing (e.g. 100 Angstroms) -- then it just copies the original mesh.  Unfortunately there is not a copy surface command, so this is a trick to copy the surface.  I need to add that command.
> 
> 	Tom
> 
> <splitsurf.jpg>
> 
> On Aug 20, 2013, at 3:26 PM, Zoltan Metlagel wrote:
> 
>> Hi everyone,
>> I've been trying to color blobs of different sizes in a tomogram by un-hiding them in order of size using the "hide dust" tool and coloring as they become visible. This has been working well and given me some insight into the structure I'm looking for, but I'm unable to restore the session to it's previous state using the "save session"/"restore session" features. The maps open fine, but all the coloring is lost. I've tried this in Chimera 1.7 and 1.8, with the same results. Am I missing something? According to the online manual, colors should be saved in a session. I apologize if this has been asked before, but I haven't been able to find the solution in the archives either. I'm otherwise very happy with Chimera, thanks for all your efforts.
>> 
>> Thanks in advance,
>> 
>> Zoltan Metlagel, LBNL
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