[phenixbb] Creating custom peptide bonds

Pavel Afonine pafonine at lbl.gov
Tue Jan 31 11:04:18 PST 2017


Hi Nick,

without seeing files I can only guess.. To me it seems that selections 
you provide are not valid (do not select any atoms, for instance). 
First, I would remove any quotation marks, that is

instead of:

chain "A" and resid "  38 " and altid "B"

use:

chain A and resid 38 and altid B

You can verify atom selection by running command

phenix.pdb_atom_selection model.pdb "chain A and resid 38 and altid B"

and it will print selected atoms to the screen.

If you are still having troubles with this please send me PDB file and 
we will investigate.

Pavel

On 1/31/17 09:47, Pearce, N.M. (Nick) wrote:
> Hi,
>
> I have a rather odd model situation, where I’m trying to manually 
> create peptide bond restraints between two alternate conformers in 
> refinement.
>
> I’m doing this using:
>
> =======
> ...
> refinement.pdb_interpretation.apply_cif_link {
>    data_link = TRANS
>    residue_selection_1 = chain "A" and resid "  38 " and altid "B"
>    residue_selection_2 = chain "A" and resid "  39 " and altid "C"
> }
> refinement.pdb_interpretation.apply_cif_link {
>    data_link = TRANS
>    residue_selection_1 = chain "A" and resid "  38 " and altid "B"
>    residue_selection_2 = chain "A" and resid "  39 " and altid "D”
> }
> ...
> =======
>
> However, running phenix.refine with this I get the error:
>
> =======
> RuntimeError: Unused apply_cif_link: TRANS ['pdbres="MET A 38 "', 
> 'pdbres="GLU A 39 “']
> =======
>
> Given that the alternate conformers have been removed from the labels, 
> I assume that this can only be used to define links between residues, 
> but not between specific conformers?
>
> Is there any way to do this?
>
> Thanks,
> Nick
>
> Nicholas Pearce
> Post-doctoral researcher
> Universiteit Utrecht
>
>
>
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