[Chimera-users] Moving individual markers

Thomas Goddard goddard at cgl.ucsf.edu
Thu Aug 2 14:19:47 PDT 2007

Hi Evan,

   One approach is to save your marker set, then open another copy of 
it.  It is not currently possible to duplicate the marker set without 
saving it.  The newly opened copy is a new marker set, with its own 
model number, and Chimera commands like "select 1", "move z 5.7", "turn 
z 30.0" could then be used to shift and rotate the copy, and the Path 
tracer dialog menu entry Actions / Transfer markers could be used to 
merge the markers into a single marker set.  That is pretty tedious.

   A better approach is to use a Python script.  I've attached one that 
copies markers from the active marker set to make any number of repeats. 
  You use it by placing markers and then just open the script with File 
/ Open to build the helix.  The helix parameters (rotation, rise, 
repeats) are set in the script.

   For schematically showing a structure "fall apart" it may be fine to 
hand move the atoms.  If you wanted it to fall apart in a defined way 
you could modify the above script to move markers instead of copy them.

   Is it ok if I post your previous message to chimera-users?


J. Evan Sadler wrote:
 > Tom,
 > I'm trying to use Chimera to make schematic 3D figures for publication.
 > One example is constructing a model of a structure, starting with a 3D
 > reconstruction from negative stain EM. I can place spheres or 
cylinders in
 > the map and make a representation of the repeating unit in, say, a 
 > tubule composed of self-assembling proteins. Knowing the axial rise 
and the
 > pitch, I could build a model by translating/rotating repeating units, if
 > that were possible.
 > Also, this particular helical tubule is held together by low pH and 
 > ions. When if falls apart, one could illustrate this by translating
 > individual markers.
 > I can do all this, rather tediously, by temporarily putting markers in
 > different sets, which can be made active or inactive for movement 
from the
 > command line. I was hoping to save a lot of keystrokes by using move 
or turn
 > on individually specified objects. The mouse of course can move 
atoms, but
 > is not precise enough for what I want to do.
 > Evan
 > On 8/2/07 1:08 PM, "Thomas Goddard" <goddard at cgl.ucsf.edu> wrote:
 >> Hi Evan,
 >>    There is no Chimera command to move individual markers (or atoms).
 >> Could you tell me in what situation you would use this capability?
 >> Tom
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