Hi Everyone,
Thank you for the advice, especially Pavel's. My issue has been
resolved. I lowered the occupancy and B-factors of the metal ions in
the .pdb and ran phenix.refine for 10 cycles. This removed most of the
negative Fo-Fc density. Anisotropic refinement of the metal ion
B-factors was
Hi Chris,
this certainly improved your model with respect to the data including
all their errors. How do you know this did not make your model worse
with respect to chemistry, respectively to what is inside your crystal?
Best,
Tim
On 05/08/2014 07:26 PM, Chris Fage wrote:
Hi Everyone,
Thank
Hi Tim,
That's a good question. The negative density vanished and the model
itself has not changed much. I still plan to set up
soaking/cocrystallization experiments with the metal ion. I am hoping
this will increase occupancy. That is the only solution that comes to
mind.
Regards,
Chris
On
/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
: [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
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
@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
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
Hi Chris,
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
Refining the occupancy will help your R-factor and flatten your density,
but you need to be careful to also refine the B-factor of the metal
ion. Don't refine both the occupancy and the B-factor during the same
run (the two are correlated at this resolution), refine the occupancy of
just the
I have used CNS before, but not for this sort of refinement. I see in
the bindividual.inp file that I can select atoms to be included--it
is defaulted at known and not hydrogen. Do you know the proper
nomenclature for selecting a Zn ion in chains A and B?
Thanks,
Chris
On 5/6/14, Steven Herron
Straightforward in Refmac...(a CCP4 package)...
From my iPhone
On 6 May 2014, at 18:02, Chris Fage cdf...@gmail.com wrote:
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
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