Hi Johannes, The "write relative" command provides this functionality, but I guess we didn't anticipate writing out structures relative to non-molecule models, so the command doesn't work when the "relative model" is a volume (we will fix this for the next release). There is a workaround. After you have positioned your structure as desired with respect to your volume, open any structure whatsoever into the same model number as your volume, then use "write relative". So, if your volume was in model 0 and the structure you want to write is in model 1, you would: position the models the way you want open 0 any.pdb write relative 0 1 transformed.pdb If you wanted to continue working and get rid of the extra structure you had to open, use the Model panel to close it ("close 0" in the emulator would close the volume also). Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Tuesday, January 21, 2003, at 07:25 AM, Johannes Fuerst wrote:

Hi there,

we are manually fitting crystal structures of proteins into cryo-EM maps with Chimera. Is there a way to read out the coordinates of the fitted crystal structure into a new pdb file, which could then be used for further refinement in other programs (ESSENS or Xplor)

Thanx for your help

Johannnes Furst Department of Biochemistry Brandeis University 415 South St Waltham, MA 02453

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