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Dear All,
I figured out that the chain ID should be contineous and the comparison
range must be defined( no default ) to run LSQKAB in ccp4, otherwise, you
will see the error message"garbage on line" as I saw. Thank you Petra
reminding me.
I appraciate those suggestions from people here, they are very useful,
especially Petra,Wollman and James Irving for giving me the link to LSQKAB
and MUSTANG. Now I fall love in LSQKAB and do all strutcure compariosns with
it. The nice thing about it is it not only reportes overall RMSD,
DP-improved RMSD, normalized RMSD( for comaprison with other alignemmt
program) but also a detailed graph of residue-residue RMSD. Below are the
links I collected:
LSQKAB: http://www.igs.cnrs-mrs.fr/Caspr2/RMSDcalc.cgi
MUSTANG: http://www.cs.mu.oz.au/~arun/mustang/
SSM: http://www.ebi.ac.uk/msd-srv/ssm/
Thanks again!
Fang Sheng
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