Correct syntax is superpose A.pdb B.pdb -o C.pdb
Doing superpose A.pdb B.pdb C.pdb will result in *multiple* structure alignment of all three structures (i.e. C.pdb ought to be an input, rather than output, file here). In general, superpose XYZ1.pdb XYZ2.pdb XYZ3.pdb ..... XYZN.pdb will do multiple aligment of all N structures. Run superpose without parameters in order to get description of all command-prompt options. Hope this helps, Eugene ________________________________________ From: Lijun Liu [lijunli...@gmail.com] Sent: Wednesday, November 19, 2014 12:17 AM To: ccp4bb Subject: [ccp4bb] superpose bug? Hi: I have a bunch of pdb files and would like to superpose them to one of them based on secondary structure matching. I would like to get a script to do so (not a one-by-one job by hand). I tried superpose but it seemed to have some problems with output option. Assuming C.pdb is the output pdb, and A.pdb and B.pdb are inputs. ============ superpose A.pdb B.pdb (this works, without output) superpose A.pdb B.pdb C.pdb (***** ERROR #15 READ:) Adding -s option get same errors (without output pdb it works). When running within ccp4i with output C.pdb, it does work. ============ I tried to generate an input script from ccp4i running. Unfortunately, running with the particular "superpose using S-S-M" option did not generate an input card (other options OK, what a bad luck). I appreciate a working script (ccp46.4.0) or a "debugged" source code for compilation. Thanks. Lijun Liu -- Scanned by iCritical.
