Re: [ccp4bb] CC1/2, XDS and resolution cut off

Dear Marcus, I have a few comments: - we do not suggest any fixed value (like 0.125) for a CC1/2 cutoff. One reason why a fixed value should not be carved in stone is that future data processing and refinement programs might extract more information from the weak data than current ones do. Ano

Re: [ccp4bb] Phenix.pdbtools Algorithm

Hi, there is Phenix mailing list for questions like this ( http://phenix-online.org/). This should answer your question: http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf Pavel On Mon, Aug 6, 2012 at 9:07 AM, Scott Foy wrote: > Hello everyone, > > I am having a difficult time

[ccp4bb] Phenix.pdbtools Algorithm

Hello everyone, I am having a difficult time determining what type of geometry regularization algorithm is used in Phenix.pdbtools (e.g., least squares, maximum likelihood, energy minimization, etc.). I would appreciate if anyone can clarify, as well as point me to the appropriate documentatio

[ccp4bb] PPI-Net Young Researchers Meeting

Dear CCP4bb, A symposium on protein-protein interactions organised by young researchers from around the UK. Will probably appeal to some from the UK, but obviously all welcome. Please respond to the organising committee (yr2...@ppi-net.org) rather than to me. Thanks Ed This symposium aims

[ccp4bb] not strictly crystallography-related

Dear all, a colleague needs a protein for a biophysical experiment. The requirement is that the protein "looks like a disk", and that it can be bought for a reasonable price. Is anyone aware of a commercially available protein of disk-like shape? I am out of ideas of how to find this out mys

Re: [ccp4bb] CC1/2, XDS and resolution cut off

> Do you think that this averaged I/sig I could also be transferred to a > averaged CC1/2 giving unobserved spots a CC1/2 of 0. > --> _all = shell_completeness * _measured? Actually yes it did occur to me (just after I hit 'send') that that would be just as valid (or invalid depending on ones POV!

Re: [ccp4bb] CC1/2, XDS and resolution cut off

Hello > Edward A. Berry wrote: > What about collecting in the corners of a square detector? > Due to the crystal diffracting better than expected or > the need to sacrifice resolution for spot separation? This is actually our reason that we have problem. The strategy initially suggested lower re

Re: [ccp4bb] CC1/2, XDS and resolution cut off

Sorry yes you're quite right, I hadn't noticed the ambiguity of 'account for': 'take into account' would have been better. -- Ian On 6 August 2012 14:39, Edward A. Berry wrote: > Oh - you meant how one could take nonrandom distrubution > into account in the analysis- > funny how I always unders

Re: [ccp4bb] CC1/2, XDS and resolution cut off

Oh - you meant how one could take nonrandom distrubution into account in the analysis- funny how I always understand what someone meant after i push send on an inappropriate reply Edward A. Berry wrote: Ian Tickle wrote: below the noise threshold. This does make the tacit assumption that the

Re: [ccp4bb] CC1/2, XDS and resolution cut off

Ian Tickle wrote: below the noise threshold. This does make the tacit assumption that the unmeasured reflections are distributed randomly in reciprocal space, which is clearly not entirely true, but it's hard to see how one could account for the non-random distribution. Again, in any case Wh

Re: [ccp4bb] CC1/2, XDS and resolution cut off

Hi Marcus I don't use CC(1/2) as a criterion for cut-off though I do keep an eye on it. It's not clear to me how you apply the CC(1/2) criterion when the data are incomplete (as they invariably are). Also there seems to be some debate whether the cut-off should be at CC = 0.5 or much lower, e.g.

[ccp4bb] CC1/2, XDS and resolution cut off

Dear all, We have in our lab a data set collected and are discussing where to cut the resolution for refinement. According to the work of Kai Diederichs and Andy Karplus one should use CC 1/2 of 12.5% (in case it is significant) to determine the highest resolution independent of the I/sigI and R f

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

Hi Peter, We're still working on the resolution of this bug. In the meantime you may wish to replace 6.3.0's scala.exe with the one from 6.2.0, which is linked to from the Windows Problems pages. Scala has not changed much between the two rele

[ccp4bb] column profile

Hi all If anyone have, please post the calibration profile for GE Sephacryl S100 26/60 Hiprep column. Sorry I could not locate in the GE Healthcare site. Thankx in advance Sajid