Dear Olga,
I have also encountered the same problem. Find below a script which will
automate the superposition of one protomer onto the others.
Best wishes
Prakash
Superposition script :-
#!/usr/bin/tcsh -f
grep -v -E '^END' Aorig.pdb > new.pdb
rm mat1.mat
foreach chain_name ( B C D E F G H I J )
# Superposition of A on chain_name
superpose Aorig.pdb tot.pdb -s ${chain_name} Aon${chain_name}.pdb | grep
-A 4 Rx >> mat1.mat
# Changing chain name to ${chain_name}
pdbset xyzin Aon${chain_name}.pdb xyzout ${chain_name}.pdb <<eof
CHAIN $chain_name
END
eof
grep -E "^ATOM " ${chain_name}.pdb >> new.pdb
rm Aon${chain_name}.pdb
end
Olga Boudker wrote:
Dear all,
I am working with a relatively low res. crystal structure with
multiple protomers in the asymmetric unit related by NCS. I am
currently running rounds manual model building in Coot and refinement
using Refmac5. Could anybody suggest a shortcut for the following
procedure: I start with an initial model containing all protomers;
generate NCS operators for A to B, A to C et c.; rebuild protomer A;
use the operators and the rebuilt A to generate all other protomers;
and combine them all in a single pdb file. Currently I do all that
manually using lsqkab and text edit and it is really painful. Is
there an available routine to do this? For various reasons I would
like to stick with Refmac5 rather then CNS, in which of course the
symmetry would have been easier to implement.
Many thanks,
Olga
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