On 02/01/2016 19:45, hari jayaram wrote:
> Hi all,
> Its been a while since I refined a structure with metal atoms. I am
> wondering what is the current best way in coot to handle LINKs beween
> Cys and Zn atoms.
>
> I have a PDB file with a whole bunch of Zincs and LINKR records. They
> are displayed in coot with all the Cys- residues SSBonded to each
> other due to proximity. ( side note If I read in a PDB file with LINK
> records ..coot does the right thing.)
I didn't know that - interesting...
The problem of SS-bond display is on the list already (quite high). Coot
needs an "Add SSBond" function.
>
> What is the best way currently ( coot 0.8 revision 5047)
!!!
> to edit these links and create them "properly". I have also not used
> the Jligand interface from inside coot and was wondering how to use
> it to clean up my Zincs.
I don't think that JLigand will be necessary.
The PDB/"proper" way is to make LINKs between the CYS and the ZN
(Extensions -> Modelling -> Make Link)
The LINKR interface in Coot is not all it could be.
>
> I am also embarrassed because I have struggled with exactly this issue
> 5 years ago (I googled and found my old questions about this :-) )
:-) but also :-(
> and I was hoping I could get a few lines of help on the best way to do
> this in the newest coot. Also I am wondering where is a good place to
> get a Zn+2 cif file from.
It should be built into Refmac (and Coot). Refinement should do the
Right Thing even though the display is messed up.
Paul.
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