[phenixbb] Green density for ligands in places where the ligand is in density

Wei Shi wei.shi118 at gmail.com
Tue Nov 5 17:10:13 PST 2013


Thank you guys for the suggestions. I changed the occupancy of the ligand
to 1 in pdb and do refinement with 'refine occupancies' box checked. The R
values dropped about 3-4% compared with before and the occupancy for the
ligand stays as 1. Thank you!

Best,
Wei


On Tue, Nov 5, 2013 at 11:17 AM, Ryan Spencer <rspencer at uci.edu> wrote:

> That is true although I think even when I changed the HETATM tag to ATOM
> and went through Phaser it still changed the unknown ligands back to HETATM
> and dropped the occupancy to 0.00. I could be wrong on this. Either way
> it’s not a big issue to edit the PDB directly or even in Coot under
> edit>residue info and set everything back to 1.00 before starting
> refinement.
>
>
>
> Ryan
>
>
>
> *From:* phenixbb-bounces at phenix-online.org [mailto:
> phenixbb-bounces at phenix-online.org] *On Behalf Of *Nathaniel Echols
> *Sent:* Tuesday, November 05, 2013 7:55 AM
>
> *To:* PHENIX user mailing list
> *Subject:* Re: [phenixbb] Green density for ligands in places where the
> ligand is in density
>
>
>
> On Tue, Nov 5, 2013 at 7:46 AM, Ryan Spencer <rspencer at uci.edu> wrote:
>
>                 The pdb of the ligand probably had an occupancy of 0.00
> when you brought it into Coot. The easiest way to handle it is to just
> change all the occupancies of the ligand back to 1.00 in the pdb. If the
> ligand has partial occupancy then phenix might be dropping it down to 0.00
> if you have the ‘refine occupancies’ box checked. I’ve seen this before
> when doing MR with ligands that phenix does not recognize without the
> corresponding .cif.
>
>
>
> That actually has nothing to do with the CIF - by default Phaser will set
> the occupancy to zero for anything labeled as a heteroatom (i.e. HETATM
> lines in a PDB file), which the exception of some non-standard or modified
> amino acids such as MSE.  It's not clear if that's what's happening in
> Wei's case; I'm pretty sure eLBOW doesn't normally output ligands with an
> occupancy of zero.
>
>
>
> -Nat
>
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