Re: [phenixbb] Unwanted LINK records

27 Jul 2019


      I tend to think to disable it globally in phenix.real_space_refine. 
Anyone affected please vote YES/NO and I will start from there.

Pavel

On 7/26/19 12:49, Ahmad Khalifa wrote:
...
I do have the same problem with the latest version. I wonder how I can 
set the anti-link option in the GUI.
Based on what does Phenix make those links? Distance?
On Fri, Jul 26, 2019, 3:09 PM Pavel Afonine mailto:[email protected]> wrote:
Hi Luca,
first off please try the latest version of Phenix and see if that
    helps.
    If it does not help, please send me the model (no data needed at this
    moment) and I will investigate.
Pavel
On 7/26/19 08:21, Luca Pellegrini wrote:
    > Hello,
    >
    > Phenix.real_space_refine generates a few spurious covalent bonds
    between protein and ligand in my structure, which distort the
    local structure, and then adds the corresponding LINK records in
    the output file. Is there a way to avoid this?
    >
    > I am aware of the anti-link option previously mentioned in the
    phenixbb:
    http://www.phenix-online.org/pipermail/phenixbb/2018-January/023677.html,
    but I was wondering if there was another way of preventing this
    from happening. I am using Phenix 1.15.2-3472.
    >
    > Best wishes,
    > Luca
    >
    > Luca Pellegrini, PhD
    > Department of Biochemistry
    > University of Cambridge
    > Cambridge CB2 1GA
    > United Kingdom
    >
    > [email protected] mailto:[email protected]
    > tel.: 0044 1223 760469
    > https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
    > @PellegriniLab
    >
    >
    >
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