Multiple occupancies using CNS

S.Ravichandran ravi at cmb2.saha.ernet.in
Tue Mar 30 00:38:15 EST 1999


Dear CNS (v0.5) users,

	Can anyone help me regarding refinement of a disordered 
sulfate ion using CNS?

	We have a 1.9 A (synchrotron) dataset for a seed inhibitor
protein. The cryo-solvent has glycerol added in the same mother-liquor
composition, in which ammonium sulfate salt is present. Because of the
salt, sulfate ions could be seen (from the tetrahedral density shape) 
in the protein's surface where the region is slightly basic in nature.

	Our problem is the following.

	Sulfate ions are found in two 'unique' places.

	In one place a sulfate ion just sits on a 2-fold axis. With 
central Sulfur atom coinciding the 2-fold axis and two of the Oxygen
sulfate atoms coincides with the other two Oxygen sulfate atoms.

	In the second place, a sulfate ion occupies 2 places. But the
distance between two sulfate ions is very short and so it is dis-ordered.

	In both the above cases, CNS complains me 'clashes'.. Because
of the short contact in their positions. 

Previously, I had no problems, when I was using REFMAC (of CCP4), in which
both DISORDER and SPECIAL POSITION atoms can be handled without any hicupps. 
But when I try to switch over to CNS, I find its a 'mess'.. 

Already, there were queries before about the usage of 'alternate.inp' in 
which one have to do some 'trick' to successfully utilize it and is not 
straightforward, as in REFMAC.

	So, why don't the authors think of some easy solution for handling
such problems?  Previously, I have written one mail to Dr. Paul Adams
of the Yale University. But till now there is no solution.

Hope someone can help me out.

Cheers,
Ravi.

PS:- Sorry for posting this question again. Since our e-mail service was
distrupted for a couple of days, I didn't get any reply.
=======================================================================
| S.Ravichandran                              e-mail:-                |
| Crystallography &                           ravi at cmb2.saha.ernet.in |
| Molecular Biology Division,                 ravichu at hotmail.com     |
| Saha Institute of Nuclear Physics                                   |
| I/AF, Bidhan Nagar, Calcutta 700 064.       FAX:-                   |
| Calcutta - 700 064. INDIA.                  (91)(033)-337-4637      |
|                                                                     |
|		URL:	http://cmb2.saha.ernet.in/ravi.html           |
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