Here's a script that will print out the RMSD "distance" matrix for an ensemble (all models have exactly the same set of atoms). To use, just run: chimera --nogui --silent your_file.pdb dm.py > matrix The output in file "matrix" should be N lines, each with N tab-separated floating point numbers, where N is the number of structures in your_file.pdb. Please let me know if that's what you're looking for. Thanks. Conrad On 7/10/12 11:32 AM, Austin B. Yongye wrote:
Hi Dr. Huang, I would like to use the "nogui" mode. Thanks a lot! Austin-
--- On Tue, 7/10/12, Conrad Huang <conrad@cgl.ucsf.edu> wrote:
From: Conrad Huang <conrad@cgl.ucsf.edu> Subject: Re: [Chimera-users] RMSD calculation To: "Austin B. Yongye" <ybausty@yahoo.com> Cc: chimera-users@cgl.ucsf.edu Date: Tuesday, July 10, 2012, 9:18 AM Will you be running Chimera with a graphical interface? If so, then the Ensemble Cluster tool already prints the RMSD matrix to the Reply Log. If you want to get the RMSD in "nogui" mode, please let us know and we can figure something out.
Conrad
On 7/10/12 7:57 AM, Austin B. Yongye wrote:
Hello Chimera-developers/users: Does someone have a script that can perform pairwise backbone RMSD calculations for a group of pdb structures in a file and write out the RMSD matrix? This may already be implemented in the clustering routine. Just need to get the RMSDs. Thanks, Austin-
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