Dear all,
I want refine my model using TLS plus phase information from experimental
phases.
I used the TLSMD server to generate the initial tls parameters and started
Refmac
After an initial round of TLS refinement Refmac stops and and claims a problem
but nevertheless writes at the end Task
===
SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS
===
Proposal application deadline: Friday, October 15, 2010
Periods:
January 1, 2011 -
On Monday, October 11, 2010 11:01:10 am Christian Roth wrote:
Dear all,
I want refine my model using TLS plus phase information from experimental
phases.
I used the TLSMD server to generate the initial tls parameters and started
Refmac
I don't know exactly what has gone wrong.
Let's
On Monday, October 11, 2010 01:04:49 pm Christian Roth wrote:
Dear Ethan,
thanks for your fast answer. The pdb file does the trick. I also did not
click
the reset B-factor box, which I thought is equivalent to the TLS+Biso pdb. Is
that wrong?
For what you are doing, it is correct to
Dear all,
Not a CCP4-related question, but there is no better informed group of people
out there.
We would like to buy a fluorometer equipped with a Peltier controlled sample
cell. We will measure Trp/Tyr fluorescence, but other groups will be using
the instrument for measuring fluorescence of
Hi Ethan,
So far as I know, there is still no provision in phenix for reading in
existing TLS parameters. It always wants to regenerate them for itself.
You are right, given suggested optimal selection for TLS groups
phenix.refine is capcabale to do the rest as good as it can. There is
Hello,
following this discussion, I was wondering how much sense it makes to use
TLS domains and experimental phases at the same time.
I would have thought that TLS domains are better to be used when the model is
fairly complete at which state the quality of the experimental phases are
probably
On Monday, October 11, 2010 12:31:13 pm Pavel Afonine wrote:
Hi Ethan,
So far as I know, there is still no provision in phenix for reading in
existing TLS parameters. It always wants to regenerate them for itself.
You are right, given suggested optimal selection for TLS groups
Hi Tim,
following this discussion, I was wondering how much sense it makes to use
TLS domains and experimental phases at the same time.
I guess both things are completely irrelevant. With using experimental
phases you bring in more data. And with using TLS you simply use a more
adequate
Hi Ethan,
yes, I must be missing something indeed...
You are missing the point.
What if you want to calculate Fcalc based on an existing model?
What if you want to explore application of the _same_ TLS model
to different sets of starting coordinates?
Yes, if I do need to calculate Fcalc
Hello Pavel,
thank you for the PDF file. When I search for the word phase starting from
page 24, all I find are phenix.phase_and_build and
phase_and_build_params.eff on p. 34, and they don't explain the problem.
I agree that experimental phases are data, but they might be utterly noisy data
and
Hi
I think you have very good point here. Towards the end of refinement (when TLS
refinement make more sense since the effects of positional coordinate errors on
B values become smaller) phased refinement refinement makes less sense
especially if phases are from density modification
following this discussion, I was wondering how much sense it makes to use
TLS domains and experimental phases at the same time.
My take on it is that if you have low resolution data, then it makes a
good deal of sense to use both experimental phases and TLS groups. But
this assumes that the
Of course if you have low resolution and good quality of phases then using
phases would improve the model (since model errors are going to be large in any
case). In this case it makes perfect sense to use TLS and phased refinement
simultaneously.
It will of course depend on resolution and the
14 matches
Mail list logo
