Hi Yuri,
If you have access to mogul you can get an understanding of what your geometry should be based on the small molecule database. Of course not everything is well represented so if your ligand is unusual this will flag up in lower statistical significance.
Mogul will allow you to understand how far you are from ideal.
Not really sure if this is what you might be after....
Joe P
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-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Yuri Pompeu
Sent: 12 September 2012 19:45
To: [log in to unmask]
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 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 complete.
What is the best way to refine the ligand unrestrained and then generate measurements?
Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)?
ANy idea is welcome.
Thanks a lot
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