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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