Here is a summary of responses to the thread I recently started on "phasing
with se-met at low resolution":
There were many suggestions. They can be grouped into two categories:
1. Aim for very high redundancy at one wavelength (peak) and watch out for
radiation damage. Sacrificing resolution is
gt;
> - Original Message -
> From: "Ethan Merritt"
> To:
> Sent: Wednesday, May 13, 2009 12:12 PM
> Subject: Re: [ccp4bb] phasing with se-met at low resolution
>
>
> On Wednesday 13 May 2009 09:30:06 Jacob Keller wrote:
> > > The reason is t
On Wednesday 13 May 2009 10:22:54 Patrick Loll wrote:
> Greg Petsko's group did something like this about a billion years ago
> (yet, strangely, I remember the paper, even though I'd be stumped if
> you asked me what I had for breakfast...)
>
> They covered the range from room temp down to ver
ct: Re: [ccp4bb] phasing with se-met at low resolution
On Wednesday 13 May 2009 09:30:06 Jacob Keller wrote:
> The reason is that you've missed out one important term: the atomic
> displacement parameters (B-factors), which describe a combination of
> thermal motion and positional di
Greg Petsko's group did something like this about a billion years ago
(yet, strangely, I remember the paper, even though I'd be stumped if
you asked me what I had for breakfast...)
They covered the range from room temp down to very cold, using
different cryoprotectants (importantly, they we
On Wednesday 13 May 2009 09:30:06 Jacob Keller wrote:
> > The reason is that you've missed out one important term: the atomic
> > displacement parameters (B-factors), which describe a combination of
> > thermal motion and positional disorder between unit cells.
>
> A somewhat niggling point: isn
The reason is that you've missed out one important term: the atomic
displacement parameters (B-factors), which describe a combination of
thermal motion and positional disorder between unit cells.
A somewhat niggling point: isn't it true that the thermal motion is
insignificant at 100K? Does an
On
Behalf Of Marc SCHILTZ
Sent: 13 May 2009 11:26
To: Kevin Cowtan; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] phasing with se-met at low resolution
Kevin Cowtan wrote:
This is absolutely correct - in the analysis you present, the
non-anomalous scattering drops with resolution, bu
Kevin Cowtan wrote:
Marc SCHILTZ wrote:
I agree with everything but would like to add the following: if we
assume an overall atomic displacement parameter, the drop-off in both
the anomalous and non-anomalous scattering is the same. Therefore, the
ratio of anomalous differences over mean in
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Marc SCHILTZ
> Sent: 13 May 2009 11:26
> To: Kevin Cowtan; CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] phasing with se-met at low resolution
>
> Kevin
Marc SCHILTZ wrote:
I agree with everything but would like to add the following: if we
assume an overall atomic displacement parameter, the drop-off in both
the anomalous and non-anomalous scattering is the same. Therefore, the
ratio of anomalous differences over mean intensity (which is what c
Kevin Cowtan wrote:
This is absolutely correct - in the analysis you present, the
non-anomalous scattering drops with resolution, but the anomalous part
does not. And since counting noise varies with intensity, we should
actually be better off at high resolution, since there is less
non-anomal
This is absolutely correct - in the analysis you present, the
non-anomalous scattering drops with resolution, but the anomalous part
does not. And since counting noise varies with intensity, we should
actually be better off at high resolution, since there is less
non-anomalous scattering to con
Dear Raja,
FOR HIGH ANGLE REFLECTIONS ANOMALOUS DATA BECOMES IMPORTANT.
Raja
this is the theoretical point of view. As James pointed out, in real life
the intensities of reflections at high resolution becomes comparable to
the noise level so that the accuracy of which the reflections a
. FOR HIGH
ANGLE REFLECTIONS ANOMALOUS DATABECOMES IMPORTANT.
Raja
From: James Holton
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, 12 May, 2009 11:26:55 AM
Subject: Re: [ccp4bb] phasing with se-met at low resolution
measuring anomalous differences has nothing
However, do not get too excited if this resolution limit is 6 A.
Although 6 A phases are better than no phases at all, have you ever
LOOKED at a 6 A map? It can be very hard to tell if it is protein or
not, even with perfect phases and all the right hand choices, etc.
If the map is a 6 Ang
Dear Engin,
On Tue, May 12, 2009 at 12:20:31PM -0700, Engin Ozkan wrote:
> The take home message for me was that noone agrees on the best data
> collection strategy
No - since you have to factor in at least half a dozen parameters:
unfortunately there is no silver bullet :-(
> Another point is t
Thanks, I do understand all of that. I gave some Rmerge and resolution
values to give some idea about errors and noise expected in the data,
and an idea for up to what resolution phases would be good. And if such
low resolution phases ever yield a meaningful model. Both measures are
flawed in
Dear James,
On Tue, May 12, 2009 at 11:26:55AM -0700, James Holton wrote:
> However, do not get too excited if this resolution limit is 6 A.
> Although 6 A phases are better than no phases at all, have you ever
> LOOKED at a 6 A map? It can be very hard to tell if it is protein or
> not, e
measuring anomalous differences has nothing to do with resolution.
measuring anomalous differences has nothing to do with Rmerge.
measuring anomalous differences has EVERYTHING to do with signal and
noise. (as does measuring anything else)
If your average anomalous difference is going to be ~5
On Mon, May 11, 2009 at 05:22:25PM -0500, Pete Meyer wrote:
> > P.S. I would also appreciate the specific query type for searching the
> > PDB on the web for phasing method (MR, MAD, SAD, MIR, etc.). They seem
> > to have everything under the sun searchable, but I cannot find this one.
>
> Last t
If experience from intrinsic zinc is ok, I'll add my two cents.
> trying). I would be happy to hear about Se-Met cases, and data
> collection strategies (2wl vs. 3wl MAD vs. SAD, etc.) and phasing
> methods used in these cases, or references of them. Again, no other
Bert already mentioned collect
On Sun, May 10, 2009 at 08:24:34PM -0700, Engin Ozkan wrote:
> The question is what would happen if your crystals diffract to 4 A,
> and anomalous signal dies at 6 A. The interesting bit of course is 1
> Met per 200 residue, which should put to death the "1 in 50" or "1
> in 100" Methionine myths:
)
Cubotron/BSP-415
CH-1015 Lausanne
Switzerland
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
Of
Engin Ozkan
Sent: Sunday, May 10, 2009 11:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phasing with se-met at low resolution
Hi everyone,
I
board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Engin Ozkan
Sent: Sunday, May 10, 2009 11:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phasing with se-met at low resolution
Hi everyone,
I thought I start a new thread while it is unusually quiet on the bb. I
am pondering over the practical
2009 5:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phasing with se-met at low resolution
Hi everyone,
I thought I start a new thread while it is unusually quiet on the bb. I
am pondering over the practical limitations to MAD and SAD phasing with
Se-Met at low resolution. What is the lowes
p4bb] phasing with se-met at low resolution
>
> Hi everyone,
>
> I thought I start a new thread while it is unusually quiet on the bb. I
> am pondering over the practical limitations to MAD and SAD phasing with
> Se-Met at low resolution. What is the lowest resolution at which p
, 2009 5:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phasing with se-met at low resolution
Hi everyone,
I thought I start a new thread while it is unusually quiet on the bb. I
am pondering over the practical limitations to MAD and SAD phasing with
Se-Met at low resolution. What is the
Hi everyone,
I thought I start a new thread while it is unusually quiet on the bb. I
am pondering over the practical limitations to MAD and SAD phasing with
Se-Met at low resolution. What is the lowest resolution at which people
have solved structures "only" using phases from selenium in a
"r
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