Thanks Randy,
so from your reply it seems that cutoff is differently treated. And if I
interpret your email correctly it is better to provide Phaser with a truncated
versus a full data set. I tried both cases, but I had assumed that if you
restrict the resolution within Phaser it would be the s
Dear Jurgen,
Thanks for your interest in DIALS - we are working hard at the moment on
testing the software and finding bugs (and fixing them!) and I would say
right now it's not quite ready for the general user, but we do plan to make
an alpha release of the software before the end of the year. Wh
Hi again,
I should have mentioned that, if you have a good enough model, it’s often
possible to solve the structure in P1. The molecular replacement solution will
settle on one of the twin domains (or you may end up with more than one
solution, related by the twin law(s)). Then the symmetry o
Hi Jurgen,
You could send me a logfile off-list, and maybe I would spot something in there.
We’ve put some effort into putting more intelligence into the Phaser search, so
that it adapts to the initial perceived difficulty of the problem in setting
the initial parameters, and then adapts to ind
Dear BB, or in particular Phaser developers :-)
This must be part of British humor right (or was that the Canadian influence
Randy) ?
eLLG indicates that placement of ensemble "ensemble_1" will be straightforward
The data are sufficient to exceed the eLLG target
The search space is finite 14
Just to follow up on this:
The enormous increase between the TFZ= and TFZ== numbers is surprising, so I
focused on that in my original answer to Fred's question. However, if anyone
wants to know the difference between these, it's documented on this web page:
http://www.phaser.cimr.cam.ac.uk/in
Hi Fred,
Send me the logfiles (off-line), because this shouldn't be happening and I'd
like to have a look. That said, we've been seeing some similar problems in
certain circumstances, i.e. B-factor refinement refines to significant negative
B-factor values, and data at high resolution have ver
Hiyya all,
I have a question about the latest Phaser output, concerning TFZ = and
TFZ == .
I do not know how to interpret outputs of the type
TFZ = 5.2 TFZ == 54.1;
TFZ = 5.8 TFZ == 63.0;
TFZ = 6.4 TFZ == 19.7 (these are real TFZ figures coming from Phaser log
files).
I used to analyse the
In a Phaser automated molecular replacement job, it does almost
everything at a working resolution and then a final refinement at a
final resolution. By default, the working resolution is 2.5A and the
final resolution is the full resolution of the data set. So the
second-last LLG is the o
I think the second LLG value is after refinement. But sometimes I see that
the second LLG goes negative and I wonder what it means. For example:
RFZ=3.1 TFZ=17.2 PAK=0 LLG=238 LLG=-603
-Konstantin
On Wed, 30 Sep 2009, Simon Kolstoe wrote:
Dear all,
In the phaser .sol file what do the two LLG
Dear all,
In the phaser .sol file what do the two LLG's correspond to on the
SOLU SET line eg
SOLU SET RFZ=20.7 TFZ=35.4 PAK=0 LLG=1699 LLG=2821
Do they show an initial and a refined LLG or do they correspond to the
rotation and translation function as in the Z scores?
I checked the app
On Fri, 13 Jul 2007, john kryst wrote:
> Hi all !!!
>
>Is it possible to fix one domain and search for the second one in
> phaser !!! What are the keywords to use.
> I have a protein with two domains. It i give both the domains together or as
> two ensembles it is not finding the solutio
Hi all !!!
Is it possible to fix one domain and search for the second one in
phaser !!! What are the keywords to use.
I have a protein with two domains. It i give both the domains together or as
two ensembles it is not finding the solution. If i give only one domain it
is giving the soluti
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