Hi George, You would have to use the MD Model tool. However, if your “concatenated” PDB file is in the correct multi-model PDB format, you can just read in that file as the trajectory… no other files (topology etc.) needed. See the “PDB, single file” input format option. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> The correct format is with MODEL and ENDMDL lines, such as used for NMR ensembles in the RCSB PDB repository (example: 1PLX). I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 28, 2015, at 8:22 AM, George Tzotzos <gtzotzos@me.com> wrote:
Hi everybody, I’m analysing the Principal Components of an Amber trajectory. I have generated a number of representative pdb files which are concatenated for each PC.
Question: Is there a way to generate an average structure in Chimera from the concatenated PDB files?
I know this can be done using MD movie but this solution requires that I generate a new topology file for my complex (the original topology file contains ligands and water molecules). Thank you in advance for any suggestions Regards George