[phenixbb] Unwanted LINK records

[Luca Pellegrini]

I disabled ‘link ligands ot protein’ in All parameters, and that fixed the problem. 

I would think that it should be off by default, but I don’t have the big picture.

Thanks all for your help.

Luca


> On 27 Jul 2019, at 09:29, Pavel Afonine <pafonine at lbl.gov> wrote:
> 
> 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 <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
>> >
>> >
>> >
>> > _______________________________________________
>> > phenixbb mailing list
>> > phenixbb at phenix-online.org
>> > http://phenix-online.org/mailman/listinfo/phenixbb
>> > Unsubscribe: phenixbb-leave at phenix-online.org
>> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
> 

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