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

[Clemens Vonrhein]

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:
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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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> > > 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/
> 
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-- 

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* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
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