Many monomers have a torsion periodicity given

Here is an extract from GLU.cif


loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 GLU      chi1     N      CA     CB     CG       180.000   15.000   3
 GLU      chi2     CA     CB     CG     CD       180.000   15.000   3
 GLU      chi3     CB     CG     CD     OE2        0.000   30.000   2

The chi1 and chi2  have targets 180 or 60 or -60  (ie periodicity 3

chi3 targets 0 or 180 - periodcity 2.

Look at you dictionary for you compound and check periodicity..
If it is already set to 2 or 3 and you drag the ligand into place COOT will then refine it to the nearest of the target values.

Is that explanation comprehensible?

Eleanor


On 24 November 2015 at 22:01, Argel Estrada <[log in to unmask]> wrote:
Dear CCP4 comunity

I would like to consult you by the next question: I am generating a pdb model which after I made a manual edition in the pdb file, incorporating an artificial aminoacid: "L-ANAP" (3-[(6-Acetyl-2-naphthyl)amino]-L-alanine (ChemSpider ID: 30647705) in a desired position. Anyway there is just one rotamer topology available from the database. Just wondering if somebody could kindly suggest me how to generate the other possible rotamers and/or load them in some program in order to minimize it?

The most of programs don’t have the choice to add a new rotamer library, then I am asking an additional request: Could someone suggest me a program able to do this? And if somebody have experience creating rotamer libraries… I’m wondering if it would be possible suggest me how to load such library in the program in order to run the minimization.

I really appreciate in advance your kind advices, commentaries and suggestion!

Thank you!


Argel.​