The simplest suggestion is to move molecule B by that symmetry operator!
But bewate - the older REFMAC uses the LINK record differently to the
PDB - it has now renamed the line as
LINKR and you should check the refmac documentation to see how to set it up.
Eleanor
Peter Chan wrote:
> 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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