Thanks a lot for all the quick replays to my post. It seems to be a
controversial topic. Bellow are to replays which more or less summarize
the answers to my post.
Cheers,
Ariel
On Wed, 2010-07-14 at 07:44 -0500, Eleanor Dodson wrote:
> Everything said is true, but one of the most important fac
Everything said is true, but one of the most important factors in
calculating structure factors and hence Rvalues is the scaling and
solvent model. All of these are pretty inadequate - probably all protein
"crystals" have large volumes of multiply ordered atoms - water
networks, alternate confo
... yes, and this is the reason why sfcheck should be replaced by a
more modern program at the Protein Data Bank!
Best regards,
Dirk.
Am 13.07.10 22:15, schrieb Ethan Merritt:
Should be in an FAQ somewhere:
Q: Why does sfcheck not reproduce my original R factors?
A: Because instead of using
Hi Ariel,
here is how the R-factor is defined and computed in phenix.refine and
related tools (such as phenix.model_vs_data):
http://cci.lbl.gov/~afonine/FandR/Fmodel_and_Rfactor.pdf
and here is the link to almost exactly the same questions asked a few
days ago on ccp4bb:
http://www.mail-
There may be several reasons:
It looks strange. Something seems to be wrong in protocols
1) Check free R flags. I have seen in few cases wrong free R.
Generally number of reflections for free should be less than for work
reflections
2) Check TLS refinement. You may need to restart TLS refinem
Hi Fred,
Also, at such a high resolution you might want to do individual atomic
anisotropic temperature factor refinement.
And unless it has changed recently, there is no such temperature factor
refinement in Phenix.
it's available in phenix.refine since 2005 or so. Please update your
vers
On Tuesday 13 July 2010 12:32:48 pm Ariel Talavera wrote:
> Hi CCP4ers,
>
> Is there any differences in the way of calculating the Rfactor between
> PHENIX.refine and other programs implemented in CCP4i, like Refmac5 or
> sfcheck, or the EDS server?
>
> I asking this because I have a structure so
Received from Peter Zwart:
> Message du 13/07/10 22:02
> De : "Peter Zwart"
> A : "Frederic VELLIEUX" , "Pavel Afonine"
> Copie à :
> Objet : Re: [ccp4bb] differences Rfactor calculations
>
> > Also, at such a high resolution
u might want to do individual atomic
anisotropic temperature factor refinement.
And unless it has changed recently, there is no such temperature factor
refinement in Phenix.
Fred.
> Message du 13/07/10 21:30
> De : "Ariel Talavera"
> A : CCP4BB@JISCMAIL.AC.UK
> Copi
Hi CCP4ers,
Is there any differences in the way of calculating the Rfactor between
PHENIX.refine and other programs implemented in CCP4i, like Refmac5 or
sfcheck, or the EDS server?
I asking this because I have a structure solved at 1.4 Å resolution.
Phenix,refine was used for its refinement and
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