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Yes, certainly, guilty as sin :) Thanks, Eugene ________________________________________ From: Tim Gruene [[log in to unmask]] Sent: Wednesday, November 19, 2014 11:22 AM To: Krissinel, Eugene (STFC,RAL,SC); ccp4bb Subject: Re: [ccp4bb] superpose bug? Hi Eugene, would you update the documentation? A canonical 'man superpose' produces superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ] where [-s CID1/2] are optional selection strings in [1]MMDB convention, and [foo_out.pdb] is an optional output file. i.e. the syntax Lijun Liu used. Cheers, Tim On 11/19/2014 10:33 AM, Eugene Krissinel wrote: > 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 > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical.