Shelx

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Experiment - Manuals

SHELX - Tutorial

   In your subfolder /Crystal_ID/Phasing/ShelX_DM, you need to have your sca file (unmerged) and some input files for ccp4 programs.

       * 1f2mtz.com (convert phases fron shelx to mtz).
       * 1s2mtz.com (convert sca file to mtz).
       * 2cad.com (combine phase and "native" data).
       * 3dm.com (to run density modification >> improve your phase).
       * 4fft.com (to calculate a map).
       * 5resolve.com (to autobuild in your map).
       * 6fft_res.com (to calculate the improved map).

      1. Run xprep on your dataset (containing anomalous signal) and follow the instructions. 
         This will create a hkl file (compatible with shelx) and an ins file.
      2. xyz.sca XPREP >> after this step you will have xyz.ins and xyz.hkl
      3. Edit the xyz.ins file (add the line NTRY 40 before HKL 3) and change the parameter 
         mind if your compound has internal distance less than 3.5A.

To run shelxd (finding Heavy Atom positions)

       * shelxd xyz
         That will create some files (Ex: xyz.lst).
         Have a look at xyz.lst and check if the peaks are redundant if yes >> it's a good sign. 
         And also check the PATFOM value.
       * Edit the ins file and add the co-ordinates of the X best peaks after find X and save the ins file.
       * Run shelxe on your data .
         You need to know your solvent content !!
         shelxe bla -s0.40 -m50
         (-s0.40 >> solvent content 40% )
         (-m50 >> 5o density modification cycles) starting from 1
       * You can improve your phases by refining the solvent content (depends on number of per 
         assymetric unit >> NCS )
       * At this point you have your xyz.phs >> hkl F PHI FOM sigF.
       * Edit the .com file, do the changes as necessary (for ex: space group, unit cell, resolution 
         limit, inuput and output name etc,.) and run them one after the other 1 2 3 etc,.
         You can check your map after the 4fft.com step.

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