Hi Albion, I believe you need to use the "Save relative to model" option in the Save PDB dialog. In that option, specify the model number of the density map. You can see the model numbers in the Model Panel (Favorites menu). Then, even if you've rotated everything around while doing the docking, the PDB file will be saved relative to the *untransformed* density map. Later when you open that original density map and the written-out PDB, the structure will be fitted to the map. This is described a little more in http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/savemodel.html I hope this helps, Elaine On Sep 1, 2006, at 11:29 AM, Albion Baucom wrote:
I have docked several models into density manually using Chimera. I saved the session, reopened it, and when I write out the docked PDB files, and read them back in, they are not oriented the same way as the model I wrote them from.
Is there something I have to do to "fix" their new orientation so when they are written out they retain this orientation?
I am using beta version 1 build 2199 01/24/2006 on a linux platform.
Thanks
Albion _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html