[phenixbb] ligand restraints

Jeff Habel jhabel at scripps.edu
Thu Aug 30 12:27:10 PDT 2007

Hi Ralf,

Thanks for both of your replies.

The case with the UNK atoms is that I have an 18 a.a. break for a loop
that runs from south to north up the back side of my protein.  About
midway there is density that clearly is not water (I have a 3 proline
stretch and I would guess that it is one of them) so I wanted to model
atoms into the density.  So in that case I would expect the UNK atoms to
behave as if they were C, N, or O.  

This is the first time I've had to deal with a synthetic ligand in a
structure so I generated the .cif file using REFMAC.  According to
Pavel's response about the UNK atoms I'll need to use elbow.builder to
generate a library file that phenix.refine can use so I guess I'll just
wait and see if elbow's .cif file "fixes" the problem with the ligand as
well.  If not, then I'll follow with your suggestion about editing the
.cif file for that torsion restraint.

I appreciate the help,


Jeff Habel PhD
Scripps Florida
Drug Discovery
5353 Parkside Dr, RF-1 Rm 102
Jupiter, FL 33458
Phone: 561-799-8849
Fax: 561-799-8957
Email: jhabel at scripps.edu
-----Original Message-----
From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Ralf W.
Sent: Thursday, August 30, 2007 2:46 PM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] ligand restraints

Hi Jeff, how do you generate the restraints for the ligand?
Could it be that the restraints dictate to co-planarity?
In that case, could you try manually removing the unwanted
dihedral restraint from the .cif file?
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