![]() There is no way I could see to specify the 1) The Chimera command script always writes ![]() These align model #1 to #0 using best matching chains (mmaker command), This command in a directory containing 3 files 3h47.pdb, 1e6j.pdb andĪlign.cmd. Show any windows, and -silent says not to show log messages. Which produces a file called "aligned.pdb" which is a copy of 3h47.pdb
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