In case it helps… After you've done unrestrained refinement, you can use
prosmart to generate external self-restraints to the current conformation
(using the -self_restrain keyword). This is flexible - you can specify residue
ranges, and it works for protein, ligand, DNA/RNA, waters, etc. These
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Dear Yuri,
at 1.18A resolution you can also refine using shelxl. It's basically
your choice on a per-atom-basis what properties you wish to restrain
and which to leave unrestrained.
With L.S. refinement and given enough RAM it can print esds of your
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri
Pompeu
Sent: 12 September 2012 19:45
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ligand geometry obs. vs. ideal
Hi everyone,
I am trying to show that a ligand underwent catalysis during a soaking
experiment.
One of the things I would like to show
I second Tim Gruene's suggestion of SHELXL; it's perfect for this.
However, there is a steep learning curve, so I strongly urge you to
pay close attention to the SHELXL (and SHELXPRO) manuals.
On Wed, Sep 12, 2012 at 11:44 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote:
Hi everyone,
I am trying to
Hi everyone,
I am trying to show that a ligand underwent catalysis during a soaking
experiment.
One of the things I would like to show is the geometry of the ligand, bond
angles/lengths, dihedrals, etc...
One of my models has a hi-res of 1.18A and the ligand density is really clear
and
You can do unrestrained refinement in refmac, at your resolution it may
be OK. If you want to keep protein restrained, you can either use
harmonic restraints or come up with a special cif-file for your ligand
with large esd targets. There is no direct way to tell refmac to
exclude specific
