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Dear Pavel, dear Garib,
how do you figure out automatically the correct flag? (I hope both
phenix and refmac will allow to manual overwrite the software's decision)
Cheers,
Tim
On 01/24/2013 07:47 PM, Pavel Afonine wrote:
Hi,
It would be nice
Dear Tim
In principle if a user defines freer flag then refmac knows about that (unless
freer flag is 0 then refmac assumes that it is default). In this case (if freer
defined by user) then it is not altered.
regards
Garib
On 25 Jan 2013, at 09:14, Tim Gruene wrote:
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is labeled 1.00 or 0.00? Or does it also check the
sets with other labels?
Cheers,
Robbie
Sent from my Windows Phone
From: Garib N Murshudov
Sent: 2013-01-25 10:46
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refmac5 vs phenix refine mixed up
Dear Tim
On Fri, Jan 25, 2013 at 2:24 AM, Robbie Joosten
robbie_joos...@hotmail.com wrote:
Phenix however needs to deal with the CCP4 type reflection binning. Now the
size of the sets cannot be used which means that you have find a smarter
solution. So I wonder how this is implemented. Does Phenix use
Dear All,
I am working on a perfectly twinned data in space group P31. when I
refine this data with phenix refine the R/Rfree is 26.6/29.4 and average
B-factor is 38.
I did one test now.
I used phenix refined pdb and refine with refmac5 and got R/Rfree of
26.2/29.7 and average
Well I am not answering your question. What is the (Wilson) B-factor of
the diffraction data ? I would personally compare the average isotropic
temperature factor of the model to that of the diffraction data.
And further the aim of refinement is not to reduce the B-factor. The aim
of
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Dear Rajesh,
first of all, a model is not true or false, it can only be
better or worse.
The explanation of what you observe depends on what you did:
- - did you use the identical and very same mtz-file as input to all
three scenarios? Some people
Yes, the wilson B-factor is comparable which is 53.6.
And also same MTZ was used for refmac5 and phenix refine, which is
processed one (original one). And also the reflections used in the
refinement was: Phenix (46793 reflections) and refmac5 (44431 reflections).
I do not know whether I answered
Dear Tim Gruene,
2013/1/24 Tim Gruene t...@shelx.uni-ac.gwdg.de
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Dear Rajesh,
first of all, a model is not true or false, it can only be
better or worse.
The explanation of what you observe depends on what you did:
- - did you use the
Dear Rajesh,
In addition to the R/Rfree, you also need to look at issues like
stereochemistry, bad contacts, clashes, the general fit into density,
unmodelled ligands/waters, Ramachandran outliers, correct side chain
rotamers etc etc. I would advice you to spend (a lot of) time visually
if they are the same, there is in principle no problem.
(you can quickly check using mtzdump)
but, just to make sure, I always use the exact same scaled and truncated
mtz-file for all refinements of any particular structure. Then there is no
doubt at all...and it is in fact easer, i.e. one less
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Dear,
of course you could ask Garib whether or not the output data were
modified by refmac5 - often they are, at least linearly scaled (which
would certainly do no harm), and unless you have read the refmac5 code
or Garib assures you I would not
PS just checked an example, and the the refmac input and output F and SIGF are
in fact NOT the same and have been subjected to something more than linear
scaling.
This was using refmac version 5.5.0109, admittedly not the newest one.
So using the refmac output mtz as input for the next run is
Dear all
As it was already stated it is essential to use the same input file (after
scaling and trancating) for all refinement sessions.
Output mtz file in the absence of twinning has been scaled to account for
anisotropic overall B values. It is modification of the data. In the twinning
Most likely scenario is that Phenix by default assigns Rfree flag as 1, while
ccp4/refmac - as 0.
That would explain your Rfree going down - because your Rfree reflections were
refined by refmac.
It would be nice if default setting was the same in different suites.
Best wishes.
On Thu, Jan 24, 2013 at 10:34 AM, Leonid Sazanov
saza...@mrc-mbu.cam.ac.uk wrote:
Most likely scenario is that Phenix by default assigns Rfree flag as 1, while
ccp4/refmac - as 0.
That would explain your Rfree going down - because your Rfree reflections
were refined by refmac.
According to
Hi,
It would be nice if default setting was the same in different suites.
it's a nice idea of course, but I feel it is impractical as it would
require changing a lot of software, both modern and legacy.
However, given array of flags it is algorithmically trivial to figure out
what is test and
Yes, Nat is right. Starting with the latest version 5.7 (that is part of ccp4)
refmac makes sure that it uses correct set for free reflections. Hopefully it
will remove some of the confusions when switching from one software to another.
refmac 5.8 version should definitely have this feature.
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