[phenixbb] About Restrain Files for ligands
Pavel Afonine
pafonine at lbl.gov
Fri Jan 8 10:16:08 PST 2021
To add to this: best way to generate restraints file within Phenix
framework is to use eLBOW with a SMILES string (using GUI or CL), then
quickly inspect the restraints file (aka 'ligand CIF file') to make sure
it reflects what you know about the ligand.
Pavel
On 1/8/21 08:02, Maxime Cuypers wrote:
> Hello,
> Naively, Perhaps the issue is that the molecule used to generate the
> .cif restraints does not have the hydrogens in the right place/ right
> hybridization?
> My suggestion would be to check it i.e. with Avogadro or any other
> chemical structure editor.
>
> Cheers
> Maxime
>
> Le jeu. 7 janv. 2021 à 14:04, Pavel Afonine <pafonine at lbl.gov
> <mailto:pafonine at lbl.gov>> a écrit :
>
> Hi Sharan,
>
> I'm guessing your are over-relying on graphic representations of
> your molecules which is discussed here to some extent:
>
> http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10
> <http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10>
>
> What really matters is that the ligand fits the map and its
> geometry matches what's expected.
>
> Pavel
>
> On 1/7/21 10:20, Sharan Karade wrote:
>> Hello all,
>>
>> I hope everybody is doing well. Happy New Year 2021!!!
>>
>> I am stuck with some unusual behavior of restrain files
>> generated by Phenix.ReadySet. I crystallized the protein with
>> ligands which have double bonds between the atoms. As I see clear
>> electron density for the ligand, I drew a ligand molecule in Coot
>> (Ligand builder) and fitted in electron density very nicely.
>> Until here, I can see the double bonds in the modelled ligand. I
>> generated the restrain files using Phenix.ReadySet to further
>> proceed for refinement. Unfortunately, after refinement the
>> double bonds were converted to single bonds. I tried to generate
>> new restrain files and refined the model, resulting in similar
>> output. But, fortunately in one case, the double bonds were
>> retained after refinement also. I tried to repeat with other
>> ligands, where I was unsuccessful to retain the double bonds.
>>
>> please help me. Thank you so much.
>>
>> Regards
>> Sharan
>>
>> --
>> Sharan Karade
>> Postdoc-fellow
>> IBBR-UMD, 9600 Gudelsky Dr,
>> Rockville
>> Maryland 20850
>>
>>
>>
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