Re: [ccp4bb] Protein-DNA covalent bond refinement

2020-07-06 Thread Pavel Afonine
Hi Cristina, in Phenix it is: Refinement settings -> Select Atoms -> Custom Geometry Restraints : you can define bonds, angles, torsions, planes, etc... Pavel On Thu, Jul 2, 2020 at 8:11 AM Cristina Machon wrote: > Dear all, > > I am writing regarding a problem we are facing with the

Re: [ccp4bb] Protein-DNA covalent bond refinement

2020-07-03 Thread Robert Nicholls
Dear Cristina, In CCP4 you've got two options that use the modern approach (Acedrg): (1) CCP4i2 -> Ligands -> Make Covalent Link. (2) Coot -> Calculate -> Modules -> CCP4. This will make a "CCP4" menu appear that contains the option: Make Link via Acedrg. Hopefully it's pretty

Re: [ccp4bb] Protein-DNA covalent bond refinement

2020-07-03 Thread Eleanor Dodson
You can create a link in COOT.. Eleanor On Thu, 2 Jul 2020 at 16:10, Cristina Machon wrote: > Dear all, > > I am writing regarding a problem we are facing with the refinement of a > structure. We would really appreciate it if anybody could suggest how to > set up geometrical restraints for a

[ccp4bb] Protein-DNA covalent bond refinement

2020-07-02 Thread Cristina Machon
Dear all, I am writing regarding a problem we are facing with the refinement of a structure. We would really appreciate it if anybody could suggest how to set up geometrical restraints for a protein-DNA covalent bond in Refmac or Phenix? Thanks in advance, Best wishes, Cristina -- Cristina