The practice at the PDB after deposition used to be to remove water alternate
position indicators - although obviously to keep their partial occupancies. I
think this was an 'undocumented feature' of the old annotation system. The new
mmCif-based annotation methods may be more adaptable.
I think there are cases where water alternate positions make sense so they
should be allowed I would argue.
All the best
Martyn
Martyn Symmons
Cambridge
----Original message----
>From : robbie_joos...@hotmail.com
Date : 23/07/2014 - 10:05 (GMTDT)
To : CCP4BB@JISCMAIL.AC.UK
Subject : Re: [ccp4bb] correlated alternate confs - validation?
Hi Bernhard,
The validation of alternates is indeed quite poor and any improvements would
probably depend on proper annotation by the depositor, particularly in complex
correlated cases.
For your model I would probably make the two waters alternates of each other.
That way, it is easier to select out one of the two alternate conformations.
Cheers,
Robbie
Sent from my Windows Phone
Van:
Bernhard Rupp
Verzonden:
23-7-2014 10:19
Aan:
CCP4BB@JISCMAIL.AC.UK
Onderwerp:
[ccp4bb] correlated alternate confs - validation?
Hi Fellows,
something that may eventually become an issue for validation and reporting in
PDB headers:
using the Refmac grouped occupancy keyword I was able to form and refine
various networks of correlated
alternate conformations - it seems to works really well at least in a 1.6 and
1.2 A case I tried.
Both occupancy and B-factors refine to reasonable values as expected/guessed
from e-density and environment.
Respect & thanks for implementing this probably underutilized secret.
This opens a question for validation: Instead of pretty much ignoring any atoms
below occupancy of 1, one
can now validate each of the network groups’ geometry and density fit
separately just as any other
set of coordinates. I think with increasing data quality, resolution, and user
education such refinements will become more
frequent (and make a lot more sense than arbitrarily setting guessed
independent hard occupancies/Bs
that are not validated). Maybe some common format for (annotating) such
correlated occupancy groups might
eventually become necessary.
Best, BR
PS: Simple example shown below: two alternate confs of residue 338 which
correlate with one
water atom each in chain B, with corresponding partial occupancy (grp1:
A338A-B5 ~0.6, grp2: A338B-B16 ~0.4).
occupancy group id 1 chain A residue 338 alt A
occupancy group id 1 chain B residue 5
occupancy group id 2 chain A residue 338 alt B
occupancy group id 2 chain B residue 16
occupancy group alts complete 1 2
. more similar…
occupancy refine
AfaIct this does what I want. True?
----------------------------------------------------------------------------------------
Bernhard Rupp
k.-k. Hofkristallamt
001 (925) 209-7429
b...@ruppweb.org
b...@hofkristallamt.org
http://www.ruppweb.org/
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