Re: [phenixbb] Unwanted LINK records

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 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 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] tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom [email protected] tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab