Hi, I am using X-plor to refine a protein structure, and now I have some questions:
1) The protein structure and its corresponding X-ray structure have four copies in one unit cell. So which way is better? A: First build up the unit cell containing four copies of the protein, then run MD under periodic boundary condition (PBC) by Xplor-NIH. B: Start with one protein copy, then define unit cell and the four symmetric operations by Xrefin, then run MD under periodic boundary condition (PBC) by Xplor-NIH. 2) How can I set up a real periodic boundary condition by Xplor-NIH, (by which command)? Thank you very much. Lizhe Xu Xu, Lizhe Graduate Student Department of Chemistry Purdue University 560 Oval Drive, Box 828 West Lafayette, IN, 47907-2084 United States Email: xulizhe at purdue.edu
