Re: [phenixbb] "standard" monomer restraints

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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Wed, Jan 10, 2018 at 3:59 PM, Pavel Afonine 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 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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