[phenixbb] "standard" monomer restraints

Nigel Moriarty nwmoriarty at lbl.gov
Wed Jan 10 17:03:15 PST 2018


It's possible that the code using using the CCP4 environmental variable to
look for monomers. Phenix (cctbx really) does have a mechanism for looking
into a user defined CCP4 library.

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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, Jan 10, 2018 at 3:59 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Which is not Phenix.. So that explains the difference.
>
> Question for Nigel is: why elbow.where_is_that_cif_file pulls cif from
> CCP4 distribution?
>
> Pavel
>
>
> On 1/10/18 14:57, wtempel wrote:
>
> $CCP4/lib
>
> On Wed, Jan 10, 2018 at 5:53 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>
>>
>> ideal O3'-C3' bond in *geo is 1.422, which interestingly matches C3*-O3*
>>> in `modules/chem_data/geostd/t/data_TD.cif`.
>>>
>>
>> This is expected. I would be worried if they didn't match. So, 1.422 is
>> what actually used.
>>
>> `elbow.where_is_that_cif_file DT` pointed me to
>>> `${CLIB}/data/monomers/d/DT.cif`, where O3'-C3' is (now, but may be not
>>> at time of *geo generation) 1.431.
>>>
>>
>> What is ${CLIB} ? I'm wondering because Phenix distribution does not have
>> "data/monomers" folders (if I remember correctly).
>>
>> Pavel
>>
>>
>
>
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