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 f' and f" values at each wavelength
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.