[ccp4bb] Refmac and links between ligands

Dear all I understand that when I use the Refmac keyword make link no Refmac should not apply found links. It keeps finding links between ligands (Na+ and ligand OH) and (I think) refines them as it issues a warning (not INFO), does not say (not be used) for these and the output .pdb file contains

Re: [ccp4bb] Refmac and links between ligands

Can you check your input file. It may contain contain link record already regards Garib On 1 Feb 2010, at 13:52, Jan Dohnalek wrote: Dear all I understand that when I use the Refmac keyword make link no Refmac should not apply found links. It keeps finding links between ligands (Na+ and

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Re: [ccp4bb] Refining against images instead of only reflections

I have re-visited these calculations over the weekend. As far as I can tell, there is just no way to change background-subtracted spot intensities with diffuse scattering unless the motions are somehow synchronized across different unit cells. Call it optical or acoustic or whatever you

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[ccp4bb] how to supply the following twin operator to detwin?

Hi All I'm having trouble with the following ... title [No title given] operator -1/2*h+1/2*k-l, 1/2*h-1/2*k-l, -1/2*h-1/2*k labin I(+)=I_Unspecified(+) SIGI(+)=SIGI_Unspecified(+) I(-)=I_Unspecified(-) SIGI(-)=SIGI_Unspecified(-) end I keep getting symmetry operator error. Thanks FR

Re: [ccp4bb] how to supply the following twin operator to detwin?

Francis, I think the only format that detwin will accept is: -h/2+k/2-l, h/2-k/2-l, -h/2-k/2 i.e. '*'s are definitely not allowed. However the matrix that is generated contains only integer elements, so in fact it won't accept the '/'s either. Is this supposed to be a merohedral (or

Re: [ccp4bb] how to supply the following twin operator to detwin?

The determinant of the matrix is zero, so it can't be a twin operator

Re: [ccp4bb] Refmac and links between ligands

Problem solved. One must also switch to the make sugar NO keyword. Otherwise Refmac tries to use the discovered sugar and ion as if it was sugar-peptide bond. Jan Dohnalek On Mon, Feb 1, 2010 at 2:52 PM, Jan Dohnalek dohnalek...@gmail.com wrote: Dear all I understand that when I use the