[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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