[phenixbb] question du jour: monomer libs where?

Nigel Moriarty nwmoriarty at lbl.gov
Wed Oct 24 12:05:22 PDT 2012


You can run ReadySet! on your model PDB to get accurate D-peptide
restraint CIFs.

Or you can use REEL to edit the L-peptide restraints.
  $PHENIX//chem_data/geostd/g/data_GLN.cif etc

Or you can run eLBOW with the three-letter code?

If the atoms are named in a similar fashion to the L-peptides
(C,N,CA,O) then the linking is automatic.



On Wed, Oct 24, 2012 at 11:36 AM, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Wed, Oct 24, 2012 at 9:40 AM, Patrick Loll <pat.loll at drexel.edu> wrote:
>> Sorry to be thick, but how then can I run a refinement job using an input PDB that contains DGL, DAS, and DPN, when files corresponding to these monomers are not found in either chem_data/mon_lib/d or chem_data/geostd/d? I see that these residues are listed in mon_lib_list.cif, but I can't find the actual restraints files.
>> I'm hoping to use one or more such files to help inform my efforts to create a modified restraints file, so my questions, albeit annoying, reflect more than mere idle curiosity...
> Amino acids (and nucleotides, and some other common monomers) live in
> chem_data/geostd, e.g. chem_data/geostd/g/data_GLU.cif.  I think you
> could turn this into D-glutamine restraints fairly easily, the key
> step being changing the chiral center to "positiv".  I'm not sure
> whether anything else needs to be done to get the chain connectivity
> working properly, however.
> Normally what you would do for a residue present in the chemical
> components but not mon_lib or geostd is run eLBOW with the
> three-letter code.
> -Nat
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
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

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