No subject

Tue Sep 25 15:04:34 PDT 2012

If the data are correctly indexed on a right handed basis system, the assig=
nment of "F+" and "F-" is such that the experimental electron density map w=
ill show amino acids and helices with the correct hand. However, if by acci=
dent a left handed system was chosen (for example if the sign of Y SCALE in=
 Denzo was chosen incorrectly), the experimental electron density map will =
have the wrong hand.=0A=
Followed by the original denzo manual:=0A=
Closer inspection of Figure 5 above should convince you that there are two =
possible "hands" to conventions. These are grouped as {1,4,5 and 8} and {2,=
3,6, and 7}. To use an X-ray film analogy, this is equivalent to looking at=
 the film either from the back side(ie. towardsthe X-ray source) or from th=
e crystal side. Denzo handles this abberation by changing the sign of the Y=
 SCALE keyword from positive to negative. If this is not done, then the ass=
ignment of the Friedel mates (Bijvoet differences) will be inverted, and th=
us the hand of the structure will be similarly inverted.=0A=
As a side note, what is the upper limit on number of Se sites Autosol shoul=
d be able to find? i have between 200 and 300 depending on the contents of =
the asymmetric unit.=0A=
Thanks again for all of the responses.=0A=
From: phenixbb-bounces at [phenixbb-bounces at phenix-online.or=
g] on behalf of Tim Gruene [tg at]=0A=
Sent: Saturday, March 22, 2014 12:08 PM=0A=
To: phenixbb at
Subject: Re: [phenixbb] xtriage reindexing suggestions=0A=
Dear Todd,=0A=
if you processed your data with XDS, you can provide the=0A=
REFERENCE_DATA_SET there. Otherwise pointless would also do what you=0A=
want and in addition aimless lists the anomalous CC of all the pairs if=0A=
you give each file a separate name in pointless.=0A=
On 03/21/2014 11:14 PM, Todd Jason Green wrote:=0A=
> Hello all-=0A=
> I am trying to merge a few partial Se datasets. I am certain that I will =
have to reindex one or more to make sure that + and - reflections are not j=
umbled up. Can someone confirm that xtriage take this into account in sugge=
sting to reindex one dataset in relation to a reference dataset? ie. does i=
t use something like maximizing the anomalous signal in suggesting whether =
or not reindexing is necessary? I think the below suggests as much but I wa=
nted confirmation:=0A=
> Automatic re-indexing=0A=
> For each data set supplied (other than the first data set given), all pos=
sible re-indexing matrices are derived as described by Grosse-Kunstleve et =
al. (2005). Each data set isautomatically re-indexed using the matrix that =
maximizes the correlation of amplitudes=0A=
> Have a good weekend.=0A=
> -Todd=0A=
> My Example:=0A=
> Reference analyses=0A=
>    The following reindexing operators have been found:=0A=
> -------------------------------------------------=0A=
> | Operator | Correlation | matches (%) | choice |=0A=
> -------------------------------------------------=0A=
> | -k,h,l   | 0.874       | 70.1        |  <---  |=0A=
> | h,k,l    | 0.032       | 76.7        |        |=0A=
> -------------------------------------------------=0A=
> If the data is reindexed with operator (-k,h,l), the correlation of=0A=
> the intensities to the reference data is maximized.=0A=
> This can be done for instance with:=0A=
>   phenix.reflection_file_converter --change_of_basis=3D"-=
k,h,l" <output_options>=0A=
> _______________________________________________=0A=
> phenixbb mailing list=0A=
> phenixbb at
Dr Tim Gruene=0A=
Institut fuer anorganische Chemie=0A=
Tammannstr. 4=0A=
D-37077 Goettingen=0A=
GPG Key ID =3D A46BEE1A=0A=

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