Automated structure determination with SOLVE
What you will need to input to SOLVE
To solve a structure automatically using SOLVE you need the following
things:
-
a solve.setup file with information on
your unit cell and resolution.
-
some raw datafiles in Scalepack or d*TREK or
just a plain text format
-
knowledge of what your heavy atoms are, and for MAD data, approximate values
of the scattering factors (f' and f") at each wavelength. The best place
to get these f' and f" numbers are from the beamline staff where you collected
your data. If you have no other source of f' and f" information,
you can use tables
of values, but this won't work as well.
How to run SOLVE
To run SOLVE, all you need to do is:
-
Set the environmental variable CCP4_OPEN to UNKNOWN with the following
command:
-
setenv CCP4_OPEN UNKNOWN
-
(You can do this in your .login_custom file if you like)
-
Choose a sample control file,
edit it to match your data, and run SOLVE with it.
-
You can watch SOLVE run by looking at the end of the "solve.status"
with "tail -30f solve.status". This file will tell you where to look
if something got typed in wrong and it will keep you informed about the
structure determination as it goes.
-
After SOLVE finishes, have a look at how to interpret your SOLVE
output.
-
If SOLVE is looking through more solutions than you want it to, and you
would like SOLVE to finish up as quickly as possible, use the solve.control
file to tell SOLVE to finish up.
-
You may want to look at the keywords that
you can use to control how SOLVE carries out its search for solutions.
-
Also have a look at what to do next such as the
ways that you can try and get more solutions
-
Have a look at how to pass your data on to
other packages after SOLVE has finished.
If you want to run solve more interactively or use it to do a host of other
things such as peaksearches on maps, converting from binary to formatted
files, or calculating coefficients for difference refinement, have a look
at the table of contents for a list
of things you can do.
You might want to try SOLVE out on some test data in your space group
using the generate
feature. This allows you
to create a MAD or MIR dataset with any heavy atom sites you want and then
run SOLVE on it. If you start with a PDB coordinate file, you can generate
a dataset, solve it, and use "O" to display the NEWEZD electron density
map that SOLVE creates along with the correct structure.