[sharp-discuss] external phase information

[Clemens Vonrhein]

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Dear Greg,

there is a mismatch between what's in the documentation and what SHARP
expects (sorry about that). The 'new' way of using external phase
information in form of HLs is:

  1. generate HLA ... HLD

  2. add these 4 columns to your existing *.data.mtz file:

     cad hklin1 old.data.mtz hklin2 hls.mtz \
         hklout new.data.mtz <<end_ip
     LABI FILE 1 ALL
     LABI FILE 2 E1=3DHLA E2=3DHLB E3=3DHLC E4=3DHLD
     end_ip

  3. select this new *.data.mtz file (as EXPERT user) - this should
     then make a few boxes appear near the bottom of the 'general'
     page.

How do you get these HLA ... HLD columns?

  - just place the PDB file as model_something.pdb into your
    sharpfiles/datafiles. On the 'Phase improvement ...' panel you can
    see a utility to extract ABCDs (near the bottom). This will do
    everything necessary (and tell you the name of the final MTZ
    file).

  - if you want to use SIGMAA/SFTOOLS: just use the 'CALC' command in
    SFTOOLS to create columns HLC and HLD with just 0.0 values (since
    you can only use PHI/FOM from the model you will only get unimodal
    phase probability - and therefore only HLA/HLB).

How to use a molrep model (in general) in SHARP?

  - you can use it as you mentioned (i.e. using the AB[CD]s in SHARP)

  - place it as model_something.pdb into your sharpfiles/datafiles
    directory and use it (for 1, 10 or all cycles) during solvent
    flattening. This will hopefully improve quality of the solvent
    envelope and therefore the power of solvent flattening.

I will update the documentation for the next release.

Cheers

Clemens

On Thu, May 29, 2003 at 09:08:24AM -0700, Gregory D. Bowman wrote:
> Hello -
>=20
> I have a partial molecular replacement solution which I would like to use=
 in=20
> combination with Se-
> MAD phases, but am having some technical difficulties. First, I cannot se=
em to=20
> get SHARP to see=20
> my mtz file, even though I have named it xxx.extern.mtz, put it in the=20
> datafiles directory, and=20
> changed my preference settings so that I am an "expert" user (I do not fe=
el=20
> like an expert user...).=20
> Actually, when I change from regular to expert mode, the "no external pha=
se=20
> information" line=20
> goes away, but is not replaced by a pulldown menu. A second problem I'm h=
aving=20
> (which may or=20
> may not be related to the first) is that I am having trouble generating t=
he HL=20
> coefficients from my=20
> pdb files: I am using sigma-a and sftools in ccp4i, but only getting HLA =
and=20
> HLB, not HLC or HLD=20
> (?!).
>=20
> Any help would be great!
>=20
> Thanks,
>=20
> Greg
>=20
>=20
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss

--=20

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park     Tel: +44-(0)1223-353033
*  Cambridge CB3 0AX, UK           Fax: +44-(0)1223-366889
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************

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