If you ask for CORR SECTion then overlapmap does just that - the CC will
have a certain value for each section regardless of the CHAIN
parameters. If you want correlation residue by residue you must ask for
CORR RESI
As someone said - a lousy model will give poor CCs even if the map is
brilliant..
But once your refinement is finished it is intresting to go back and
check the CC of the initial maps.
There is a belief that you need a CC of >0.5 to be able to build the
structure but different problems and different builders achieve
different results..
Eleanor
Hailiang Zhang wrote:
Hi,
I am working on a real space correlation on a specif protein section using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map \
mapin2 ${PDB}-2.map \
mapin3 ${PDB}-mask.map \
<<eof
CORR SECT
CHAIN A $START $END
END
There is no error message, but the results make no difference no matter
how I change $START and $END. I am not sure whether the above script is
ok.
By the way, more importantly to me, if corr sect works at all, will it
print out a single CC value by integrating over the WHOLE region define by
the section range?
Thanks!
Best Regards, Hailiang
