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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Fri, Jul 26, 2019 at 12:51 PM 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

...

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

On 7/26/19 08:21, Luca Pellegrini wrote: 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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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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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