[sharp-discuss] Re: sharp-discuss Digest, Vol 19, Issue 6

[Joanne Lemieux]

On August 14, 2006 05:00 am, sharp-discuss-request at globalphasing.com wrote:

Hi,

We do not have this option in our version of sharp 3.4.0:

>   4. there should be a pull-down menu, where you now can select your
>      newly created *.hatom file

Under the 1. general heading, at 1.5 we see:  No of expected sites and 
chemical element. Does something need to be done at the installation level in 
order to see this option? Any help would be appreciated as many in our lab 
use sharp and this option would be useful.

Thanks in advance,
Joanne

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> Today's Topics:
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>    1. Re: phase extension (Clemens Vonrhein)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 14 Aug 2006 08:46:03 +0100
> From: Clemens Vonrhein <vonrhein at globalphasing.com>
> Subject: Re: [sharp-discuss] phase extension
> To: Noinaj <noinaj at uky.edu>
> Cc: sharp-discuss at globalphasing.com
> Message-ID: <20060814074603.GF31125 at laue.globalphasing.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Nick,
>
> usually I would always use autoSHARP with all reflections, since it
> tries to automatically decide what a good resolution cut-off for the
> HA-detection is. However, especially in SAD the analysis for deciding
> on this resolution cut-off can be a bit unreliably. The it is
> recommended to start with a lower resolution.
>
> Once you've found some HA sites (in autoSHARP or outside ... doesn't
> matter), I recommend the following:
>
>   1. create a file with extension .hatom in your sharpfiles/datafiles
>      directory
>
>   2. edit it to hold the fractional coordinates of your HA sites (the
>      ones you trust), e.g.
>
>      ATOM Se 0.1234 0.2345 0.3456
>      ATOM Se 0.4567 0.5678 0.6789
>
>   3. start autoSHARP using the full resolution range
>
>   4. there should be a pull-down menu, where you now can select your
>      newly created *.hatom file
>
>   5. make sure to tell autoSHARP the maximum number of Se-atoms you
>      expect per monomer! autoSHARP will try and complement the found
>      HA sites, since you might not have found all of your Se sites.
>
> Hope that helps ...
>
> Cheers
>
> Clemens
>
> On Sat, Aug 12, 2006 at 04:19:04PM -0400, Noinaj wrote:
> > Hi,
> >
> > I have found Se sites using autoSharp with resolution limits 30-6.0
> > angstroms (as suggested by NOTES within autoSHARP).  Yet my actual
> > dataset (as well as native dataset) is up to 2.4 angstroms.  What is the
> > best approach to do phase extension to higher resolution cutoff within
> > SHARP/autoSHARP?
> >
> > Could I use the initial sites that I find from ha search and then refine
> > and phase using highest resolution cutoff of 2.4?
> >
> > Thanks for all your advice in advance!
> >
> >
> >
> > Cheers,
> > Nick
> >
> >
> >
> >
> > ________________________________________
> >
> > Nicholas Noinaj
> > University of Kentucky School of Medicine
> > Department of Molecular and Cellular Biochemistry
> > Biomedical Biological Sciences Research Building, Rm 236
> > 741 S. Limestone
> > Lexington, Ky 40536
> > Lab:  859-323-8183
> > Home:  859-228-0978
> > noinaj at uky.edu
> > www.noinaj.com
> >
> >
> > _______________________________________________
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> > sharp-discuss at globalphasing.com
> > http://www.globalphasing.com/mailman/listinfo/sharp-discuss

-- 
M. Joanne Lemieux, Ph.D.
Medical Science Bldg., 429
Department of Biochemistry
University of Alberta,
Edmonton AB
Canada T6G 2H7
ph(lab):      780-492-2422
ph(graphics): 780-492-0610
fax:          780-492-0886
joanne.lemieux at ualberta.ca
http://xray.biochem.ualberta.ca/~joanne/