[phenixbb] Unwanted LINK records
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
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>
> 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.
>> 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
>> 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
>> Unsubscribe: phenixbb-leave at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb