This almost does what you want, but not quite.
To quote from the NCS6D manual:
"NCS6D uses a set of BONES or PDB atoms as input and tries to find a set
of rotations and translations which maximise the correlation coefficient
between the density at the (BONES) atoms and those at the same atoms
after application of the operator."
So you cannot use a mask in NCS6D - you can in IMP.
In the case where I did something like this, I could see a single helix
near the SeMet sites, so I built this helix, then used the following
script to find the first NCS relationship:
#!/bin/csh -f
#
/usr/local/Uppsala/rave_osx/osx_ncs6d << EOF
eden_400.ext
P
ncs6d_probe.pdb
1
p21212.sym
30.5 6.5 23.0
Y
0 359 10
0 179 10
0 359 10
-10 10 2
-10 10 2
-10 10 2
L
rt_best.o
EOF
Then I wrote a little C program that broke out each of the 100-or-so NCS
operators that are in rt_best.o into files called rt_test_NN.o
(NN=integer) and ran each and every one of them through Imp:
#!/bin/csh -f
#
#
foreach file (rt_test_*.o)
\rm LOG
/usr/local/Uppsala/rave_osx/osx_imp MAPSIZE 35000000<< EOF >! LOG
eden_400.ext
model.mask
p21212.sym
$file
Automatic
1.
.02
2.0
.1
.01
.0001
2
Proper
Complete
Quit
rt_test_new.o
EOF
set cc = `grep "Correlation Coefficient" LOG`
echo $file
echo $cc
end
#
I guess you could create a "fur ball" of Calpha positions for the
initial model to force NCS6D to sort of a volume average - or peak-pick
the map around the Se sites - I have not tried this. I found that
without the IMP step there were too many similar and unimpressive
solutions for the NCS operator and the top one was not in general the
correct one.
This approach has the potential to consume quite a lot of CPU but the
initial map was relatively ugly and ultimately it worked rather well.
Others might have more elegant ideas.
Phil Jeffrey
Princeton
Partha Chakrabarti wrote:
Hi,
Apologies for a non CCP4 question in strict sense. I am trying to work
out the NCS operators for a three wavelength
Se-MAD data which has only one site. The map is hardly interpretable.
I came across the USF Rave package and what I am aiming is
creak a mask around the heavy atom site (found by SHELX or Solve)
using mama or so, (ideally from resolve.mtz but not necessarily),
translate it to the other heavy atom site(s),
give a 6d search with NCS6d and
perhaps refine the best CC a bit with imp.
If it works, I could try use the NCS operator in DM or Resolve etc.
I was wondering if someone has a C-shell scripts for dealing with such
situation already. Of course if there are other programs for such a
task within CCP4, could give it a try.
Best Regards,
Partha
