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 [[log in to unmask]]
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
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