Re: [ccp4bb] Double covalent ligand

[Rob Nicholls - MRC LMB]

Dear Rens,

CCP4i2 now contains a CIF dictionary accumulator, which should help with 
handling such problems (note it's also available as standalone to be used via 
command line if that's useful). This is used automatically when providing 
multiple ligand CIF dictionaries to the Refinement interface. You might want to 
check out this article, which gives an overview of the various options for 
dealing with covalent linkages within the CCP4 suite, along with advice and 
discussion to help you decide which solution is best in your case: 
https://scripts.iucr.org/cgi-bin/paper?ir5021

Regards,
Rob



> On 16 Sep 2021, at 15:53, Vries, Rens de  wrote:
> 
> Dear all,
> 
> I was wondering if there was a good way to generate a restraint file for 
> ligands that are covalently bound to two sites of the same protein. Just to 
> clarify, the ligand can be viewed as a "bridge" between two residues of the 
> same protein monomer. 
> 
> At present, I use JLigand to prepare the separate links (so two separate 
> files). However, you can't combine both CIF files without software running 
> into errors. If I use either the ligand CIF (without links) or the CIF of the 
> singly covalent version, the refinement will still work fine, because the 
> LINK in the PDB file is present. But I'm wondering if there is no better way 
> to do this.
> 
> Thanks in advance,
> 
> Rens
> 
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[ccp4bb] Double covalent ligand

[Vries, Rens de]

Dear all,

I was wondering if there was a good way to generate a restraint file for 
ligands that are covalently bound to two sites of the same protein. Just to 
clarify, the ligand can be viewed as a "bridge" between two residues of the 
same protein monomer.

At present, I use JLigand to prepare the separate links (so two separate 
files). However, you can't combine both CIF files without software running into 
errors. If I use either the ligand CIF (without links) or the CIF of the singly 
covalent version, the refinement will still work fine, because the LINK in the 
PDB file is present. But I'm wondering if there is no better way to do this.

Thanks in advance,

Rens



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