[phenixbb] About Restrain Files for ligands

[Sharan Karade]

Hi Pavel, and Maxime

Thank you so much for your valuable suggestions. I will try to generate the
restrain file as you suggested and re-run the refinement.


Regards
Sharan

On Fri, Jan 8, 2021 at 1:16 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> 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> 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
>>
>> 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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>
>

-- 
Sharan Karade
Postdoc-fellow
IBBR-UMD, 9600 Gudelsky Dr,
Rockville
Maryland 20850
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