?? Refmac knows because of the group definition, otherwise I cannot
force grouped occupancy refinement. There is no definition in PDB
that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of
(whatever) residue/water.
BR
-----Original Message----- From: Tim Gruene
[mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014
15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re:
[ccp4bb] correlated alternate confs - validation?
Hi Bernhard,
do you refer to the PDB who, according to Martyn, remove the altloc
indicator? That's certainly a serious bug that should be fixed as
quickly as possible.
Within refmac the preservation is fine and as you would expect it
to be: altA only sees atoms in altA and those witout altLoc, etc,
which makes sure you PDB file is interpreted correctly by refmac5.
That's how I refmac works.
Best, Tim
On 07/23/2014 03:26 PM, Bernhard Rupp wrote:
I would probably make the two waters alternates of each other.
Quite possible, but the group definition, i.e. to which alt
conf. side chain they belong,
would need to be preserved, too.
BR
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?
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