[phenixbb] Unwanted LINK records

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jul 26 13:27:54 PDT 2019


There is an option to control this, link_ligands, that defaults to True.
You should be able to set it to false by search for it in the parameter
list.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Fri, Jul 26, 2019 at 12:51 PM Ahmad Khalifa <underoath006 at gmail.com>
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 <pafonine at lbl.gov> 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
>> >
>> > lp212 at cam.ac.uk
>> > tel.: 0044 1223 760469
>> > https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
>> > @PellegriniLab
>> >
>> >
>> >
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