Hi Mingfeng, Each "snapshot" should start with a MODEL record and end with an ENDMDL (not END), see the description of "PDB, single file": http://www.cgl.ucsf.edu/chimera/1.2304/docs/ContributedSoftware/movie/ framemovie.html MD Movie will use the MODEL numbers as frame numbers, so they should start with 1 or 0 and increment by 1. Most NMR structures in the PDB that include multiple models are done this way, so you could look at those as examples. I hope this helps, Elaine ----- 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 On Feb 5, 2007, at 8:08 AM, Mingfeng Yang wrote:
Dear Chimera users and developers,
I'd like to use chimera to view the motions of a protein. If all the snapshots are to be saved in a single PDB file, what's the correct format for them?
I tried the following, but chimera complained that a single structure is included only.
Thanks, Mingfeng ------------------ MODEL 1 ATOM 1 N ALA 1 -4.564 -7.956 -6.531 1.00 0.00 N ATOM 2 CA ALA 1 -5.237 -8.746 -5.532 1.00 0.00 C ATOM 3 C ALA 1 -4.360 -9.172 -4.378 1.00 0.00 C ... ATOM 81 HN ALA 10 0.195 11.398 3.736 1.00 0.00 H END MODEL 2 ATOM 1 N ALA 1 - 5.031 -8.234 -5.174 1.00 0.00 N .... END _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users