Hi Matt, If the new structure is sufficiently well matched to the old one when they are in the default (untransformed) positions, then after you reset to the various positions, you can bring the new one in by applying the same transform as is used for the older similar structure. For example, if your older similar structure is model 3 and the newer one is model 10, and you have just reset to a position that leaves the new model stranded, try the command matrixcopy 3 10 to bring 10 into the proper position. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html> How "reset" dealt with new models not in the original saved position was improved (after release 1.3) so that the new models will maintain their transformation relative to the lowest-numbered model that was included in the position. I guess your older similar model is not the lowest-numbered. Or, if it is, you could try using a recent daily build. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 2, 2009, at 1:52 PM, Matthew Dougherty wrote:
I am trying to incorporate a new pdb structure into an existing session file that has a number of savepos view_names.
The new pdb file that is pretty much the same as the old pdb file, just a few side chains moved. So in reset default, they are pretty much sync'd up.
when I try some of the other view_names, the new pdb structure does not match. Its as though the same transformations used in the old PDB structure are not being applied to the new PDB structure.
How can I sync the new PDB structure to the various view_names?
thanks, Matt