I believe the OP was asking how to best make an "element density map"
where the map value is proportional to the occupancy of not just any
anomalous scatterer, but a specific element of interest. For example,
suppose you have Zn and Ni in your protein, but you are not sure which
atom is which. If
I forgot to say in my email about the program AnoDe that of course it
also uses the FA values from the SHELXC output file name_fa.hkl as the
amplitudes for the 'heavy atom map' with phases (native-alpha). This
procedure is remarkably simple and effective.
George
On Thu, Jul 07, 2011 at 09:46:37A
Dear Jacob,
Andrea Thorn and I will be demonstrating such a program (called AnoDe) at
the Software Fayre at the IUCr Meeting in Madrid and it is already available
from my beta-test site on email request. AnoDe requires only two input
files: a PDB file of the refined structure and the name_fa.hkl f
It'll depend on your data, but you'd probably be better off using the
inflection (rather than peak) and remote datasets for dispersive
difference maps. This signal is usually fairly weak to begin with, and
not using the infection datasets weakens it further.
Pete
FWIW - my understanding is
There are tools out there that calculate such a map.
REVISE is one - I guess i is in the list of CCP4 programs.
i often do both maps independently and look at them for common peaks
The trouble is that dispersive differences are often less reliable than
the anomalous ones..
Eleanor
07/06/20
On Wednesday, July 06, 2011 10:36:20 am Jacob Keller wrote:
> > That would be an approximation of the map it seems you actually want,
> > which would use the F_A amplitude terms from MAD analysis together
> > with your current model phases rather than the MAD phase estimates.
> > You could, for exa
> That would be an approximation of the map it seems you actually want,
> which would use the F_A amplitude terms from MAD analysis together
> with your current model phases rather than the MAD phase estimates.
> You could, for example, use CAD to merge the FA column output by
> hkl2map with the ph
On Wednesday, July 06, 2011 09:46:14 am Jacob Keller wrote:
> Dear Crystallographers,
>
> it seems to me that for clearly identifying/characterising anomalous
> scatterers for a solved structure, one could make a map using two
> datasets: one at the f" peak, one low energy remote.
That would be
4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller
[j-kell...@fsm.northwestern.edu]
Sent: Wednesday, July 06, 2011 5:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model
Phases
Dear Crystallographers,
it seems to me that f
Dear Crystallographers,
it seems to me that for clearly identifying/characterising anomalous
scatterers for a solved structure, one could make a map using two
datasets: one at the f" peak, one low energy remote. One would then
use the signal both from the Bijvoet differences in the peak dataset
pl
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