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CCP4BB  July 2008

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Subject:

Refinement problems with links between atoms in different asymmetric units in Refmac5‏

From:

Peter Chan <[log in to unmask]>

Reply-To:

Peter Chan <[log in to unmask]>

Date:

Fri, 25 Jul 2008 17:20:27 +0100

Content-Type:

text/plain

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text/plain (45 lines)

Good Day,

This is my first post on ccp4bb, and I am seeking advice on a problem I have
encountered.

My crystal structure revealed a nickel ion chelated by 4 nitrogen atoms: 3
from protein chain A and 1 from chain B.  A and B form dimers.  The nickel
was placed in the same asymmetric unit as chain A, and it is linked to the
chain B from a different asymmetric unit.

The space group is P21 21 21, and from coot, it shows that the symmetry
operation required to bring chain B in contact with the nickel ion of its
asymmetric unit is:

[X+1/2, -Y+1/2, -Z + (0 0 1)]

According to http://www.genome.ad.jp/dbget-bin/www_bget?pdb+1UBQ (at REMARK
290) and from my understanding, this corresponds to the code 4556 (from 4555
+ the 001 translation).

Based on http://www.wwpdb.org/documentation/format23/sect6.html, I believed
I could specify this link by including the following into my pdb file:

LINK        NI    NI M   1                 NE2 HIS B 103     1555   4556

However, when I run Refmac5 of ccp4i6.0.2, this line appears to be
completely ignored by the program.  On the other hand, the 3 contacts
between Ni and chain A were all detected and refined with no problems, as
the previous cycles of refinement have generated such a line in the pdb file:

LINKR        N   HIS A   2                NI    NI M   1                HIS-NI

Under "Setup Geometric Restraints" in Refmac5, I have attempted to
check/uncheck the "Links between symmetry related atoms" option, and tested
it in combination with All others if "defined in file only and/or residues
are close".

So far, I have no luck in getting Refmac5 to recognize this bond.  Are there
obvious things that I may have missed?  Or did I do something completely wrong.

Any comments/suggestions would be greatly appreciated.

Regards,

Peter

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