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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:
> [log in to unmask] 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
>
> [log in to unmask]
>
> [log in to unmask]
>
> http://www.ruppweb.org/
>
> -----------------------------------------------------------------------
>
>
>
>
>
>
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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