In my experience ADIT (or ADIT2) is aware of symmetry mates,
and gives a different message for waters related to them- something
about these waters will be moved for you if you don't do it yourself.
I would go ahead and deposit, and when you are given the final file
to OK for release, if it erroneously indicates isolated waters
point out the error to your helpful annotator.
(actually someone from pdb or pdbe will
probably post a reply shortly).
eab
Petr Kolenko wrote:
No.
Some of them have 2.7 AA contacts to main chain!, some of them are in
second, or third solvatation shell. And they are not distributed
around some special area. It is somehow random.
Thanks anyway!
Petr
2011/6/22 Charles Allerston<charles.allers...@sgc.ox.ac.uk>:
Are they bound to the symmetry-related molecule?
cheers,
charlie
Dr. Charles Allerston
Genome Integrity Group
Structural Genomics Consortium
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 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 deposition, but just ignored three or four reports, because I
knew, I was doing the right thing. Does anyone know how to solve this problem?
I have already tried:
- changing HETATM to ATOM
- assigning different chain ID for waters to have same ID as protein chain
- renumbering of residues (not in this case, but the previous one)
I do not have to solve this problem, but I do not want to have so strange
Validation Report from ADIT.
Many thanks for any idea.
Petr
PS: Not important, but refined with REFMAC5 at medium resolution.
--
Petr Kolenko
kole...@imc.cas.cz
http://kolda.webz.cz
