I havent a reference for the "correct" value of the CC - it is just
based on maps I have seen solved then checked out later.
but if your final model gives a very poor CC with a map calculated from
experimental phases, either for parts of the structure, or for the
whole, it is time to worry. Maybe your phases are bad - poor
measurements, low solvent content, incorrect heavy atom sites, etc.
Or maybe your model has some serious errors?
But of course all crystal structures have some parts better ordered than
others and for those bits the exptlly phased map may have weak density,
espec. after solvent flattening.
eleanor
zhan...@umbc.edu wrote:
Hi Eleanor:
Do you have some references in mind that discussed the value of CC (say
0.5) to be able to build the structure? Didn't find one for right now:-(
By the way, probably a "weak" question, In the case "a lousy model will
give poor CCs even if the map is brilliant", we still accept this model
dispite the poor CC, right? Sorry that I didn't get practically involved
too much in real model building, but I just heard that model is more
frequently built manually by eyes, not CC etc.
Best Regards, Hailiang
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
