[sharp-discuss] Re: Heavy Atom Negative Density

[Clemens Vonrhein]

Dear Paul,

> I had thought about that, especially with the Hg
> derivative. However, that anomlous signal, weak as it is, proves
> that the FeS cluster is still there. Also, the Hg crystal is still
> the same colour as before soaking; though, the Os crystal is black
> (even after a long de-soak).

Before looking at your electron density map (before or after solvent
flattening?) I would recommend looking at the residual maps:

 - since your MAD data seems to be kind of ok (and you're using it as
   a reference) I assume, that the ANO residual maps for each of your
   MAD wavelengths are more or less empty - especially AT the Fe
   sites? Any only positive (or only negative) density at all Fe sites
   of a given wavelength would otherwise indicate wrong f'' values ...

 - now have a look at the ANO residual maps for the Os and/or Hg
   dataset. Since you now specified the FeS sites (with the proper
   f'/f'' values for the wavelength they were collected at?) you can
   do the same check as with each of the MAD wavelengths, ie make sure
   that the residual maps are clean and there is no all positive (or
   negative) density at the sites - indicating wrong f'/f''

 - have a look at the ISO residual map for your OS and/or Hg
   derivative (ie isomorphous differences between Os derivative and
   the reference = first MAD wavelength): nice and flat?

 - are the occupancies and/or B factors (if refined) very different
   for your Os/Hg derivatives when compared to the MAD?

 - if all these checks are ok (and now comes the 'magic' bit ...):

   - in the Preferences page (from the main SHARP Control Panel)
     specify yourself as an 'Expert' user

   - start a new SHARP job based on your latest and best SHARP run

   - switch off  ML refinement (keep everything else the same)

   - 'Save only' it !!!!

   - edit the new .sin file that was written in your
     sharpfiles/cardfiles directory and add the following line (in the
     top bit, before the 'ATOMS {' line:) left justified:

     SPECIAL         HINMAP  

     (before going into a long explanation what this does etc - lets
     first see what happens, ok?).

   - from the main SHARP Control Panel (after a Netscape 'Reload')
     request a 'Restart' of this new SHARP run (remember the job id of
     the file you just edited). This will just start the SHARP job
     using your edited SIN file.

   - cross your fingers ... and let me know what the electron density
     maps look like now ...

 - if in doubt: just attach your SIN file(s) to an email for me ...

Cheers

Clemens

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