[chimera-dev] Placing Chimera markers

[Thomas Goddard]

Hi Karin,

   There is no programming documentation for Chimera markers and marker 
sets.

   You can place a marker at position p = (x,y,z) using

	import VolumePath
	VolumePath.place_marker(p)

Its radius and color and which marker set it is placed in and whether it 
is connected to an already selected marker is determined by settings in 
the volume path tracer dialog.  If you don't want to use tho`se dialog 
settings you can instead use code like:

	xyz = (5.2, 1.2, -4.2)
	rgba = (0,0,1,1)  # red, green, blue, opacity in range [0,1]
	radius = 2.0
	mset.place_marker(xyz, rgba, radius)

Here mset is a marker set.  You can get the current marker set shown in 
the path tracer dialog using code:

	from VolumePath import volume_path_dialog
	d = volume_path_dialog(create = True)
	mset = d.active_marker_set
	if mset == None:
	  mset = d.new_marker_set_cb()

All of the marker routines are in

	chimera/share/VolumePath/gui.py
	chimera/share/VolumePath/markerset.py

The markerset.py file defines the Marker_Set, Marker, and Link classes 
that hold the path data.

The marker positions are obtained using

	mlist = mset.markers()
	for m in mlist:
	  print m.xyz()

Markers need not be connected.  If they are connected they need not be 
in a single path.  Three or more links can connect to a single marker. 
To find the links use:

	llist = mset.links()
	for link in llist:
	  m1, m2 = link.marker1, link.marker2 # the two linked markers
	  print m1.id, 'connected to', m2.id

Hope this gives you some ideas to start with.  Sorry for the poor 
quality of the path tracer code.  Suggestions for improving it are welcome.

	Tom

Karin Gross wrote:
> Hi Tom,
> 
> I have some questions concerning the makers and markersets in chimera.
> 
> First of all, is there any programmer documentation for the markers?
> 
> I want the users to be able to place markers directly onto my plane. Is there
> any possibility to get the coordinates for each marker and place markers with
> specific x-,y-, z- coordinates?
> 
> The next feature I want to offer is, that the user is able to define a
> path(connected markers) within a volume and then the plane should follow this
> path  through the volume.
> Therefor I need some infomations about the paths, how they are stored?, can I
> get out the path for moving my plane onto it?, etc...
> 
> Thanks for your time
> -Karin
>