[phenixbb] "standard" monomer restraints

wtempel wtempel at gmail.com
Wed Jan 10 14:36:24 PST 2018

Thank you for the hints, Pavel.
ideal O3'-C3' bond in *geo is 1.422, which interestingly matches C3*-O3* in
`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.
How does phenix resolve which ideal values to use in the TD example?


On Wed, Jan 10, 2018 at 3:47 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Wolfram,
> how/where (in the PHENIX installation tree?) can one look up target values
>> (effective during restrained refinement in PHENIX) for specific bond
>> lengths and angles of monomers like amino acids or nucleosides?
> If you know three-letter code:
> elbow.where_is_that_cif_file ATP
> or simply look at the file content directly in
> chem_data/mon_lib/
> or in
> chem_data/geostd
> or
> inspect *.geo file (always created in refinemetn) that lists all
> restraints used in refinement.
> Pavel
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