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SOLVE/RESOLVE Home |SOLVE Home |SOLVE Table of Contents | Solve Index

Sample scripts for SOLVE

Choose one of the following sample control files, edit it to match your data (you may need to check on data formats), 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.

If you want to change some parameters that are not listed in this file you should have a look at the list of keywords for SOLVE automated operation.

Each control file also comes with a script you can use to generate a dummy dataset and an output solve.prt file that will be similar to the one you should get if you run the control file on the dummy dataset. (Note: it won't necessarily be identical, because slight differences between machines can lead to somewhat different output files. The overall answers are usually about the same, though. The files here were generated on a DEC alpha.) You can use these to make sure everything is working properly.

Note in particular the keywords

• READDENZO/READFORMATTED/READTREK
• UNMERGED/PREMERGED
• READ_INTENSITIES/READ_AMPLITUDES

LABIN / HKLIN (for CCP4 files, see example ccp4 MAD or MIR scripts)

ADDSOLVE and ANALYZE_SOLVE. Note also if you know some of your sites at the beginning you can tell SOLVE to use them:

• under "lambda 1" or "derivative 1" specify
• atomname xx    ! xx is your atom
• xyz x y z           ! coordinates of this atom
• .. more xyz values
•  before ANALYZE_MAD or ANALYZE_MIR or SAD specify:
• ADDSOLVE    !  ADDSOLVE (add on more sites) or ANALYZE_SOLVE (refine input sites)
• SOLVE will refine these sites and go on from there.
• See sample solve.com file for ADDSOLVE.
• See sample solve.com file for ANALYZE_SOLVE.

Single datasets

Command files for running SOLVE with...

• 1 SAD dataset: generate one or solve one or look at the solve.prt output from generate followed by solve.
• 1 MAD dataset: generate one or solve one or look at the solve.prt output from generate followed by solve.
• 1 MIR dataset: generate one or solve one or look at the solve.prt output from generate followed by solve.
• 1 MIR dataset with anomalously scatter ing atoms in the native: generate one or solve one (requires version 1.10 or higher) or look at the solve.prt output from generate followed by solve.

Multiple datasets

If you have several types of datasets on the same crystal, then you can combine them into one pseudo-MIR dataset (see also the documentation on COMBINE). You can also analyze MAD data with more than one type of anomalous scatterer with this method. Edit these control files for combining datasets (Note: all these require version 1.10 or higher):

• MAD + MIR datasets: generate one or solve one or look at the solve.prt output from generate followed by solve.
• 2 MAD datasets: generate one or solve one or look at the solve.prt output from generate followed by solve.
• 2 MIR datasets: generate one or solve one or look at the solve.prt output from generate followed by solve.
• 1 MAD dataset with 2 anomalously scattering atoms: generate one or solve one or look at the solve.prt output from generate followed by solve.