[phenixbb] "standard" monomer restraints

Paul Adams pdadams at lbl.gov
Wed Jan 10 17:11:32 PST 2018


Is this intended though? I had assumed that elbow.where_is_that_cif_file command would return the cif file that Phenix would use. 


> On Jan 10, 2018, at 5:03 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
> 
> 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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-- 
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
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