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

Ryan Spencer rspencer at uci.edu
Tue Nov 5 08:17:16 PST 2013

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.




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.



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