Yes - mlphare did, but so does Phaser_ep
E
On 16 December 2013 18:46, Bosch, Juergen jubo...@jhsph.edu wrote:
Didn't mlphare use to print those values in the log file ?
Jürgen
On Dec 15, 2013, at 4:29 PM, David Schuller dj...@cornell.edu wrote:
I have some SIRAS data of a known structure. I
Hello David,
I would use the SAD target function of refmac5 for the anomalous
occupancy. As of isomorphous occupancy and phasing power, I don't know.
Best,
Tim
On 12/15/2013 10:29 PM, David Schuller wrote:
I have some SIRAS data of a known structure. I want to get the
isomorphous and
I would find the sites from the PHIC - you need to use CAD to add
Fcalc PHIC and FOM to the original data with Fnative Fderiv DANOderiv
etc
I usually then use SCALEIT to scale native and derivative to Fcalc -
then you know you are roughly on an absolute scale
Then feed those sites into Phaser_EP
Didn't mlphare use to print those values in the log file ?
Jürgen
On Dec 15, 2013, at 4:29 PM, David Schuller
dj...@cornell.edumailto:dj...@cornell.edu wrote:
I have some SIRAS data of a known structure. I want to get the
isomorphous and anomalous occupancy and phasing power from my data.
I have some SIRAS data of a known structure. I want to get the
isomorphous and anomalous occupancy and phasing power from my data.
What's the best software to do this?
--
===
All Things Serve the Beam
Hi Pu
Obviously your SAD SIRAS solutions can't both be right, one must
have the inverted handedness: I would guess it's the SIRAS solution
that's wrong, since the SAD solution seems to have given you an
interpretable map. The reason for getting the wrong hand in the SIRAS
case is probably that
Maybe I need to elaborate on Ian's answer.
SHELXD or other heavy atom location programs based on Patterson and direct
methods have a 50% chance of getting either heavy atom enantiomorph,
and in addition different solutions may be related by allowed shifts of
the cell origin (8 in P212121).
Dear Pro. George,
Many thanks for your detailed and clear exposition, which gives me a more
clear idea about this question (Although I still don't really understand the
basc mathematic things behind it).
I rechecked the sharp logs, and found that the original SAD sites were
wrong, which
MAD and SIRAS will in general behave like SAD. However if your isomorphous
difference is large and the anomalous signal is lost in the noise, they
might be dominated by it and so tend to behave more like SIR.
I thought that MAD and SIRAS had no hand ambiguity--not true?
Jacob Keller
Not true. For MAD and SIRAS you still have to try both hands of the heavy
atom substructure (unless the heavy atom arrangement is itself
centrosymmetric, then both hands are correct).
Maybe I should also mention for completeness, that for the space groups
I41, I4122 and F4122 the heavy atoms
Dear Pu,
sorry for the long(ish) answer ... handedness/enantiomorph, heavy atom
sites and consistency (while using SHARP/autoSHARP) are just one of my
favourites ;-)
On Fri, Aug 20, 2010 at 01:39:58PM +0100, Pu Gao wrote:
I rechecked the sharp logs, and found that the original SAD sites
were
Dear all,
My case seems to have two factors: 1. origin choice. and 2.
handedness/enantiomorph.
And this kind of problem seems to be very common during the experimental
phasing process. And I learned a lot informations both theoretical and
practical from your replies.
Many thanks for all
Dear Pu,
If I may add a few remarks those already made by George and Clemens, I
would say that you cannot expect two heavy atom solutions obtained in
separate runs of SHELXD (or any other substructure solution program) from
two distinct sets of differences to be consistent with each other in
Dear Eleanor at al,
On Fri, Aug 20, 2010 at 05:20:05PM +0100, Eleanor Dodson wrote:
There is quite a lot of background to these Qs in a variwty of text
books, and something on this website.
http://www.ccp4.ac.uk/dist/html/pxmaths/index.html
Nice page :-)
When changing hand you need to
The present generation of high throughput structural biologists stays on the
intellectual shoulders
of the giants of crystallography from past days (modifying GOOGLE). In the
military jargon, in the constant wars with the
structures, situation described in this exchanges is called encounter.
Hi all,
I recently solved a structure using SAD or SIRAS successfully (refinement using
native data). But I came across some questions about the heave atom (Hg) sites.
SG : P212121. Cell: 61.000 137.700 142.170 90.00 90.00 90.00 (native and
derivative are very similar).
1. I used shelxD
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