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

[Joanne Lemieux]

On August 15, 2006 12:38 am, Clemens Vonrhein wrote:
Thanks Clements.
 I figured this out after I put the hatom file into the datafiles directory.

Thanks again
Joanne

> Dear Joanne,
>
> this option appears as soon as you have a file with the *.hatom
> extension in your sharpfiles/datafiles directory (with the right
> permissions).
>
> Cheers
>
> Clemens
>
> On Mon, Aug 14, 2006 at 12:21:13PM -0600, Joanne Lemieux wrote:
> > 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:
> > >
> > >    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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> >
> > --
> > 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/
> >
> > _______________________________________________
> > sharp-discuss mailing list
> > 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/