LSQKAB error: you have failed to find any atoms to fit

From: sreetama das
Date: 3 February 2012 09:28

Dear All,

             I am trying to superpose 2 chains from the same pdb file. I have generated 2 separate pdb files, each with one chain, using PDBSET.
When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it fails to run. The 2 input files CONTAIN the columns for occupancies and B-factors. ( some old mails in the BB mention checking if these columns are present)

details of the error are:
############################
OPEN FILES AS REQUESTED
opening coordinate file of model to be moved
Logical name: XYZIN2  File name :/abc/def/../../*2.pdb
pdb file is being opened on unit 1 for input
Matrices derived from CRYST1 CARD in COORDINATE FILE
                RF                                                RO
matrices .....

logical name: XYZOUT filename: /abc/def/../../*12.pdb
pdb file is being opened on unit 2 for output

opening coordinate file of fixed model
logical name:XYZIN1 filename:/abc/def/../../*1.pdb
pdb file is being opened on unit 3 for input

MAtrices derived from cryst1 card in coord. file
            RF             RO
matrices...

FORMATTED    UNKNOWN file opened on unit 7
logical name: RMSTAB, filename :/abc/def/../../*_rmstab.graph

FORMATTED    UNKNOWN file opened on unit 8
logical name: DELTAS, filename: /abc/def/../../*_deltas.log

** ZERO OCCUPANCIES IN WORKING SET**  0.0
** ZERO OCCUPANCIES IN REFERENCE SET**  0.0
LSQKAB: ***ERROR - YOU HAVE FAILED TO FIND ANY ATOMS TO FIT ***
##############################################

Any idea how to fix the problem?

Thanks in advance,

regards,

sreetama