[sharp-discuss] hatom file output

[Clemens Vonrhein]

Dear Roni,

the 'proper' format is

ATOM Se 0.1234 0.2345 0.345

the important bits:

  - the first four characters need to be 'ATOM'

  - the atomic symbol should be (UPPERCASE)(lowercase), so 'Se' and
    not 'SE'

  - the coordinates are fractional

  - the amount of white-space between items can be anything (but maybe
    not TABs or such things)

See also:

  http://www.globalphasing.com/sharp/manual/chapter4.html#GLIST
  http://www.globalphasing.com/sharp/manual/autoSHARP1.html#datafiles

 ---------------------------------------------------------------------

So how can you get this file? If you found your sites with e.g. SHELXD
you will have a *.res file with already fractional coordinates. If you
have a PDB file, I would do

  coordconv xyzin your.pdb xyzout your.frc <<e
  INPU PDB
  OUTP FRAC
  e

and the fractional coordinates (your.frc) will have the fractional
coordinates in columns 2-4. This assumes that your input PDB file has
a correct (!) CRYST1 card.

 ---------------------------------------------------------------------

As you can see from

  http://www.globalphasing.com/sharp/manual/autoSHARP1.html#datafiles

you can use PDB files directly in autoSHARP (note column
13-16!). autoSHARP will rename your starting *.hatom file (in PDB
format) into *.hapdb and create a new *.hatom file - basically just
running the coordconv step described above.


Does that make sense?

Cheers

Clemens


On Tue, May 29, 2007 at 10:53:02AM -0400, Roni Gordon wrote:
> Hi all,
> 
> Just trying to figure out where to find / how to produce the hatom file
> that's required to skip the HASEARCH step in autoSHARP.  The manual
> talks about orthogonalizing a PDB-style file, but I figured that SHARP
> would simply produce a file that I could pump back in... or is this
> meant to be done via the site editor?  
> 
> Any help would be appreciated.
> 
> Roni
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 

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