Re: [ccp4bb]: A SAD case... - Summary

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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OnLineHelpForm wrote:
> 
> I am using ccp4 version  release-4_2_1.
> I am using ccp4i.
> My compiler is: native
> I installed using compilesource
> The problem is as follows:
> 
> Thanks to all who responded!
> 
> I leave a brief summary of all replies with a few comments, it seems that
> I have not yet worked out why my selenium atoms are in the middle of
> the solvent.  I have tried almost all suggestions but regrettably with
> no success, and I would like to try changing the origin of the output
> pdb file, could perhaps someone explain how to do it?


Did you say what your space group was?

Yes - you did - P212121..

There is a table of alternate origins for all spacegroups attached - it
should be in $CLIBD but I cant remember where !


 Here is an extract..

 530: Number of Alternate origins for Spacegroup:  P 21 21 21          
is:   8
 533: Norigin     Ox      Oy      Oz
 534:       1  0.0000  0.0000  0.0000
 535:       2  0.0000  0.0000  0.5000
 536:       3  0.0000  0.5000  0.0000
 537:       4  0.0000  0.5000  0.5000
 538:       5  0.5000  0.0000  0.0000
 539:       6  0.5000  0.0000  0.5000
 540:       7  0.5000  0.5000  0.0000
 541:       8  0.5000  0.5000  0.5000

You can change origin using the symgen key word of pdbset
pbset xyzin old.pdb xyzout shift.pdb
symgen x+1/2,y+1/2,z say would move your coordinates..

 BUT - it is  unlikely you need to do this ..
RESOLVE will generate a map starting from the SE sites you used , and
they should be on the same origin as your map..

 Are you sure the SnB sites and the SOLVE sites are on the same origin
and hand.
It is pretty easy to recognise this from the fractional coordinates and
the symmetry operators unless your spacegroup has very high symmetry..

 There are ways to do it with programs but more fun by hand!

 .

.....
> 
> - Phil Jeffrey suggested doing an anomalous difference Fourier phased with
> the DM phases (assuming the DM phases were reasonable, as they looked so),
> and perhaps also peak-picking the RESOLVE map to obtain the right peaks.
> Oddly enough, peak-picking produced peaks mostly on top of the main
> chain's density, while the anomalous difference Fourier produced peaks
> onto the SnB calculated peaks, which I find most confusing.

 Not so surprising - the RESOLVE map wants to show the protein, and will
have flattened the SE sites..

It is good that the DANO map reproduces your Se sites..

Are you displaying the map with all symmetry generated? The simplest
explanation is that your Se sites have symmetry equivalent positions 
within the RESOLVE density and you are not displaying all the equivalent
sets..

> 
> - Eleanor Dobson and Gottfried Palm hinted at the possibility that the
> origin of the substructure could be shifted with respect to the map's
> origin.  Could someone explain how to produce all the origin-shifted
> pdb's?  The space group is P212121.
> 


 See above - prob. not necessary..

Eleanor