[Chimera-users] not able to 'transfer markers'

Thomas Goddard goddard at cgl.ucsf.edu
Mon Feb 5 11:51:19 PST 2007

Hi Jeff,

   Menu entry "Actions / Transfer selected markers to current set" in 
the path tracer dialog moves the markers to the marker set chosen on the 
first line of the path tracer dialog.  That should be the same as the 
one chosen in the marker set scrolling list (Features / Marker set list) 
unless that list has multiple sets selected.

   The error message "Markers in one set cannot link to markers in a 
different set" means you tried to transfer some markers to the current 
set but they were connected by at least one link to markers in another 
set.  That is not supported.

   There is a command, keyboard shortcut "sc" that extends the current 
selection to all markers connected to currently selected ones.  You'll 
need to turn on keyboard shortcuts with main window menu entry Tools / 
General Controls / Accelerators On.  You can have them turned on by 
default every time you start Chimera using the Preferences dialog (menu 
Favorites / Preferences) category Tools and clicking the check button in 
the autostart column next to "Accelerators On".

   One possible confusion about hiding/showing markers is that if you 
have any markers selected then the Actions / Show & Hide menu entries 
act on those selected ones no matter what marker set they belong to.  If 
there are no markers selected then those same menu entries act on all 
markers in the current marker set, that is the one chosen at the top of 
the path tracer dialog.

   The marker set scrolled list is used for closing multiple marker sets 
and for saving multiple marker sets.  This may have been the problem 
when you could not close a marker set.  It closed the one selected in 
the scrolled list which was different from the "current marker set" 
shown at the top of the path tracer dialog.  When you change the current 
marker set menu it unfortunately does not clear the selected marker sets 
in the scrolled list.  That is a bug.

   Let me know if you can reproduce the problem hiding/showing markers.


Jeff wrote:
> hi Tom,
> using build 2318, if I select a series of markers, and then click 
> 'actions -> transfer selected markers to current set', it gives the 
> error 'Markers not transfered. Markers in one set cannot link to markers 
> in a different set.' when I did this, I assumed that the 'current set' 
> meant the one selected in the 'marker sets' dialog box in the volume 
> path tracer.
> is there a way for me to get around this? I had traced out a series of 
> actin filaments in one set, and for practical reasons want to be able to 
> show/hide each marker path that corresponds to a filament; the only way 
> I could think of doing this was to have each filament be a separate 
> marker file, unless there is a command that allows me to select a single 
> marker and then just 'display markers connected to selected marker' 
> (preferred, actually), as opposed to using the up-arrow, which selects 
> the entire set.
> after performing the 'transfer markers' request, I was no longer able to 
> show/unshow the marker sets. Also, when I closed a marker set, it was 
> still displayed. I shut down the session and recreated it from scratch. 
> I'll let you know if this show/unshow/close marker file issue occurs 
> again and under what circumstances; it would be hard for me to claim 
> that it was correlated to the 'transfer markers' command, I just know 
> that after that point in the session I could no longer show/unshow/close 
> the markers.
> thanks,
> -Jeff

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