-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear James,
your explanation is the background of the strong advice to always
build as much as possible before running the next refinement cycle.
I've seen directories with way more than one hundred runs of refmac
and don't want to know what has been
John, can you give me a good reference on this?
-- Ian
On 21 November 2012 07:32, Jrh jrhelliw...@gmail.com wrote:
Ian, yes absolutely but your very description of where the unit cells are
not identical is NOT the situation where we see fractional occupancy
moieties. In such cases a large
Dear Pavel,
Also worth mentioning the obvious that the mathematical functional form of an
occupancy and a B factor in its -ve exponential is very different BUT at lower
resolutions they behave similarly. Thus higher resolution refinement allows an
'easier' determination of each parameter.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Robbie Joosten
Sent: Tuesday, November 20, 2012 6:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] occupancy vs. Bfactors
Hi Grant,
This is part
: Re: [ccp4bb] occupancy vs. Bfactors
Hi Grant,
This is part of the recurring side chain discussion.
There is no consensus in the community about what the optimal approach
is.
In your current approach
@JISCMAIL.AC.UK] On Behalf Of Pavel
Afonine
Sent: Monday, November 19, 2012 3:54 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] occupancy vs. Bfactors
Hi Grant,
sounds like you did the right thing (as far as I can guess given the amount
of information you provided).
In a nutshell
PS: Partial occupancy is not the same as disorder. You can have
well-ordered different occupancies that manifest themselves then in
superstructure patterns. Common in small molecule/materials.
Hello Bernhard
Agree with everything you said up till this point, but I think the owners
of the
Nomenclature hazard warning:-
Ian, Thankyou for drawing attention to the nomenclature school:-
Partial occupancy disorder
Which I prefer to refer to as
Partial occupancy order.
Outside our MX field static disorder refers to what we call split occupancy
order. I like the latter and dislike the
John
Having begun my crystallographic life with small molecules (organic
semiconductors) and subsequently moved to PX, and having worked on SOD
crystals I stand in both camps (i.e. both meanings: site-occupancy disorder
and superoxide dismutase!). It seems to me that static disorder is the
Something you want to be very careful with here that appears to have not
been mentioned yet is phase bias.
If you have built in a wrong side chain or other entity that is not
actually there, but still force it to have occupancy=1 and reasonable B
factors (B factor restraints might do that)
Ian, yes absolutely but your very description of where the unit cells are not
identical is NOT the situation where we see fractional occupancy moieties. In
such cases a large fraction of the unit cells ARE ordered. QED. John
Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair
Hello all,
I'm currently working on a structure which if I stub a certain side chain
phenix/coot shows me a large green blob which looks strikingly similar to the
side chain, when I put it in and run another refinement the blob turns red.
Basically I was just playing around and I changed the
Hi Grant,
sounds like you did the right thing (as far as I can guess given the amount
of information you provided).
In a nutshell, both, B-factors and occupancies, model disorder. The
difference is that occupancies model larger scale disorder (such as
distinct conformations) than B-factors
that would be a better model.
HTH,
Robbie
Date: Mon, 19 Nov 2012 23:36:56 +
From: gdmi...@students.latrobe.edu.au
Subject: [ccp4bb] occupancy vs. Bfactors
To: CCP4BB@JISCMAIL.AC.UK
Hello all,
I'm currently working on a structure which if I stub a certain side chain
phenix/coot shows me
14 matches
Mail list logo
