[sharp-discuss] sharp output (eden.mtz)

Clemens Vonrhein vonrhein at globalphasing.com
Fri Mar 16 13:24:30 GMT 2007


Hi Dylan,

you can't calculate residual maps using the eden.mtz. For residual
maps you need to use the resid.mtz. See

  http://www.globalphasing.com/sharp/manual/appendix1.html#resid

for an explanation of the columns in resid.mtz and an example how to
use them in CCP4 FFT program. Same for

  http://www.globalphasing.com/sharp/manual/appendix1.html#eden

to calculate electron density maps - although you might want to first
do density modification (after deciding on the correct hand!) instead
of looking at maps from HA phasing directly.

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

If you run SHARP/autoSHARP in the default way (i.e. through the
httpd-based SERVER), then all this is completely automated anyway:
very easy to look at residual maps, doing density modification and
looking at electron density maps. When running autoSHARP through the
CCP4i interface you should have created files (basically tar-files)
that contain all those maps already for you.

So I'm not sure why you need to use eden.mtz/resid.mtz by hand at all
- I never do this.

Cheers

Clemens



On Fri, Mar 16, 2007 at 09:16:54AM -0400, Dylan Murray wrote:
> Clemens,
> 
> Sorry for the delay in my response.  I should have been more clear in  
> my description of the problem.  My eden.mtz file contains entries that  
> look like:
> 
> 
>     0   0   4        2.00    305.42    180.00      0.87     -0.51      0.00
>                      0.51      0.00    351.46      4.18     -1.33      0.00
>                      0.00      0.00      1.40    305.93    180.00      0.87
>                    305.93    180.00      0.00   -180.00
>     0   0   4        2.00    351.99    180.00      1.00      0.41      0.00
>                      0.41   -180.00    352.20      4.20     -4.06      0.00
>                      0.00      0.00      4.06    351.58    180.00      1.00
>                    351.58    180.00      0.00   -180.00
>     0   0   4        2.00    298.50    180.00      0.85      0.17      0.00
>                      0.17   -180.00    352.02      4.20     -1.25      0.00
>                      0.00      0.00      1.33    298.33    180.00      0.85
>                    298.33    180.00      0.00   -180.00
>     0   0   4        2.00      4.91    180.00      0.01      0.04      0.00
>                      0.04   -180.00    351.93      4.20     -0.01      0.00
>                      0.00      0.00      0.69      4.87    180.00      0.01
>                      4.87    180.00      0.00   -180.00
>     0   0   4        2.00    226.55    180.00      0.64     -0.42      0.00
>                      0.42      0.00    351.73      4.19     -0.77      0.00
>                      0.00      0.00      0.96    226.97    180.00      0.64
>                    226.97    180.00      0.00   -180.00
> 
> So you see it appears that SHARP has output several different results  
> for an hkl that all differ slightly.  I have used this file in FFT  
> (CCP4) to make a residual map, but I have not had a chance to look at  
> it.  There are no apparent errors in the FFT output.  I just can't  
> tell which set of columns FFT is using for each hkl.
> 
> Thanks for any help.
> 
> Dylan Murray
> 
> Quoting Clemens Vonrhein <vonrhein at globalphasing.com>:
> 
> >Hi Dylan,
> >
> >the way MTZ files are organised, they can hold up to 500 'columns' per
> >reflection. There are always the same number of columns for each
> >reflection record in the MTZ file - although sometimes you might have
> >MNF (missing number flag) for some data items (represented as '?' if
> >you run MTZDUMP on the MTZ file). For a detailed description of the
> >MTZ format please see
> >
> >  http://www.ccp4.ac.uk/dist/html/mtzformat.html
> >
> > ---------------------------------------------------------------
> >
> >If you want to know what column is what in the eden.mtz, see:
> >
> >  http://www.globalphasing.com/sharp/manual/appendix1.html#eden
> >
> >and for resid.mtz:
> >
> >  http://www.globalphasing.com/sharp/manual/appendix1.html#resid
> >
> >The interesting columns for you should be:
> >
> >  eden.mtz:
> >
> >    FP/SIGFP        : 'native' amplitude and sigma
> >    HLA,HLB,HLC,HLD : phase probability (Hendrickson-Lattmann
> >                      coefficients)
> >    Fcent/PHIcent   : amplitude/phase for map (light atoms only)
> >    FB/PHIB         : amplitude/phase for map
> >
> >If you let me know what the next step is you want to do I could tell
> >you how to use these files. If you run SHARP/autoSHARP through the
> >httpd (highly recommended) you will not need to bother about what
> >column is what: all the extra tools take care of that (residual map
> >analysis, density modification, looking at maps with Coot, O, Xfit
> >etc).
> >
> >Cheers
> >
> >Clemens
> >
> >
> >On Tue, Feb 13, 2007 at 03:06:57PM -0500, Dylan Murray wrote:
> >>Hello,
> >>
> >>I am looking at the mtz output (both eden.mtz and resid.mtz) from
> >>SHARP and am rather confused.  The mtz files contain multiple entries
> >>for each reflection.  Are things supposed to be this way?  What do the
> >>multiple entries mean?  Why are there five for some hkl and only two
> >>for others?
> >>
> >>Thanks for any help.
> >>
> >>Dylan Murray
> >>
> >>
> >>_______________________________________________
> >>sharp-discuss mailing list
> >>sharp-discuss at globalphasing.com
> >>https://www.globalphasing.com/mailman/listinfo/sharp-discuss
> >>
> >
> >--
> >
> >***************************************************************
> >* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> >*
> >*  Global Phasing Ltd.
> >*  Sheraton House, Castle Park
> >*  Cambridge CB3 0AX, UK
> >*--------------------------------------------------------------
> >* BUSTER Development Group      (http://www.globalphasing.com)
> >***************************************************************
> >
> 
> 
> 

-- 

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



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