On 05/07/2014 10:52 AM, Tim Gruene wrote:
At 2.5A resolution (the resolution this thread is about)
But maps ae not made "at 2.5 A" but from say 30A to 2.5 A.
In principle (i.e. if the 0,0,0 reflection were used), the effect
of diminishing the amplitude of high resolution terms is not to
decrease the total electron density but to smooth the features:
If the electron density profile going through the atom were a
rectangular box, the sharp corners would be rounded resulting in
less density inside the box and more outside, with the integrated
electron density the same. Which is exactly what you would expect
for an atom with increased rms displacement.
Now when the 0,0,0 reflection is absent so that the map is "floating"
with average value zero, and also the object is smaller than the
bragg spacing of the reflection, the 2.5 A reflection may contribute to
total electron density - I'm not sure.
Still the main effect of increasing the B factor should be to
spread out the density, while decreasing occupancy reduces
the total electron density without affecting the shape.
I can readily imagine that refinement programs can successfully
deconvolute the two. 90% correlation may be manageable.
eab
On 05/07/2014 10:52 AM, Tim Gruene wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Dear Bernhard,
I just happen to collect the correlation between ADP and occupancy for
a publication I am involved in.
At 1.5A (!) resolution, the correlation for a single ion between both
figures is greater than 90% - there is certainly not a clear
difference between these factors.
One of the reasons might actually be visualised from the URL you
posted: At 2.5A resolution (the resolution this thread is about) the
number of electrons for Zn with B=30 drops from 30 to 25, which is not
so great a difference, at 1.5A it drops to about 20, which is still
not so great a difference, i.e. the B-factor weight is not too far off
from being constant at 'protein' resolution ranges.
Best,
Tim
On 05/07/2014 02:58 PM, Bernhard Rupp wrote:
the negative difference density surrounding your metal ion shows
that the lower occupancy could not be fudged by a higher
B-factor
Because there is a clear difference between high B-factor and low
occupancy: High B factor attenuates high resolution scattering
most, while lower occupancy just evenly scales the scattering curve
down. Ergo, the FT - the Electron density - also looks different,
with a low occupancy causing a WIDER scattering curve than a
comparable high B-factor, thus transforming into a NARROWER peak
compared to high B-factor.
So, you could adjust (within physically meaningful limits) B and n
to 'reshape' the electron density. If you have a negative
difference density 'ring', your 'observed' density there is less
than the model density, and by reducing n you could reduce the
wings of the model electron density peak, thus achieving a better
match.
There is also the possibility that you have - perhaps in addition -
some truncation ripples, which are most prominent around heavy
atoms.
Figures 9-6 and 9-5 BMC. This app allows to generate the different
scattering curve shapes, and a similar app lets you FT it.
http://www.ruppweb.org/new_comp/scattering_factors.htm
Best, BR
-----Original Message----- From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi.com Sent: Mittwoch, 7. Mai 2014 14:25 To:
CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: [ccp4bb] Refining Metal
Ion Occupancy
Dear Chris,
In my experience, modern refinement program manage quite well to
deconvolute occupancy and B-factor. In your case the negative
difference density surrounding your metal ion shows that the lower
occupancy could not be fudged by a higher B-factor. I would just
refine occupancy and B-factor at the same time and let the
refinement program do the deconvolution. If your density maps would
still indicate problems, you always can try to manually
deconvolute.
By the way, your formulation <attempt to "flatten" the negative
density> sounds like some cheap trick, when in fact you try to get
a model that more accurately reflects your observed diffraction
pattern.
Best, Herman
-----Urspr�ngliche Nachricht----- Von: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Chris Fage Gesendet:
Dienstag, 6. Mai 2014 19:03 An: CCP4BB@JISCMAIL.AC.UK Betreff:
[ccp4bb] Refining Metal Ion Occupancy
Hi Everyone,
In my 2.5-angstrom structure, there is negative Fo-Fc density
surrounding a metal ion after refining in Phenix. From anomalous
diffraction I am certain of the metal's identity and position in
each monomer. Also, the ion is appropriately coordinated by nearby
side chains. Should I be refining the occupancy of the ion in
attempt to "flatten" the negative density? I am considering soaking
the metal ion into crystals or cocrystallizing and collecting
additional datasets.
Thanks for your help!
Regards, Chris
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/
iD8DBQFTakicUxlJ7aRr7hoRAq9bAKCZURDNZxvfzuXpk0slF1vh6hkkLACfd5Ls
s7OV453Zj63k1xMOo+qzTfA=
=lpSS
-----END PGP SIGNATURE-----
