Dear Petr,
Did you try WHAT_CHECK? It has a number of tests for water and will take
indirect interactions with the macromolecule into account.
Cheers,
Robbie
Date: Wed, 22 Jun 2011 16:01:45 +0200
From: arnaud.goepf...@unibas.ch
Subject: Re: [ccp4bb] Waters in ADIT
To: CCP4BB@JISCMAIL.AC.UK
Dear colleagues,
I want to deposit one structure, but ADIT reports tens more waters
that are further than 3.5 AA away from macromolecule atoms. I
inspected about half of them manually, but all of them are OK. I have
observed this incorrect behavior of ADIT also in one previous
structure for
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr
Kolenko
Sent: 22 June 2011 12:18
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Waters in ADIT
Dear colleagues,
I want to deposit one structure, but ADIT reports tens more waters that are
further than 3.5 AA away from macromolecule atoms. I inspected
On Wed, 2011-06-22 at 14:10 +0200, Petr Kolenko wrote:
Some of them have 2.7 AA contacts to main chain!
it may be a good idea to report this to the PDB, this seems like a
bug.
--
Hurry up before we all come back to our senses!
Julian, King of Lemurs
Nuffield Department of Medicine
Old Road Campus
University of Oxford
OX3 7DQ
http://www.sgc.ox.ac.uk/
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr
Kolenko
Sent: 22 June 2011 12:18
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Waters in ADIT
Dear Petr,
I guess ADIT only looks for interaction between water molecules and the protein
and does not take into account the interactions between water molecules. So if
a water molecule interacts with another water molecule but not with the
protein, ADIT will give you these error report even
