SHARP/autoSHARP Tutorials	previous next
Chapter 2

Step-by-step explanation for running autoSHARP

(MAD/SAD or SIR(AS)/MIR(AS) experiment with known sites)

Since the steps are nearly identical to the ones outlined in Chapter 1, only the sections that are different are described here.

Preparation
Input files
Setting the job up
Analysing the log file
What to watch out for
Fine-tuning

2. Input files

heavy atom sites
This can be either in our own format (using fractional coordinates) or as a PDB file (which uses orthogonal coordinates). In both cases (but especially in the case of a PDB file) make sure that the atom type i given correctly. So you might need to edit a PDB file to have correct atom types in the atom name column (column 13-16). Please note that the PDB file should also be named something.hatom!

3. Setting the job up

See Chapter 1 - Setting the job up.

If the heavy atom file was placed correctly into the sharpfiles/datafiles directory (with the correct naming convention), it should show up as a selectable item in the General (SAD/MAD) or derivative (SIR/MIR) section(s).

Submitting the job

See Chapter 1 - Submitting the job.

4. Analysing the log file

See Chapter 1 - Analysing the log file.

5. What to watch out for

Check that the sites given by your heavy atom sites file are taken correctly into the first SHARP refinement (problems in reading the file or format conversion can always happen).

6. Fine-tuning

See Chapter 1 - Fine-tuning.

Last modification: 18.11.04