Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test

2008-02-22 Thread Kay Diederichs
Ulrich Baumann schrieb: It is a known feature that data sets integrated with previous XDS versions had frequently cumulative intensity distributions that could be interpreted as twinning, i.e. the number of weak reflections was too small and the curves for the acentric reflections had a sigmoid

Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test

2008-02-22 Thread Ulrich Baumann
It is a known feature that data sets integrated with previous XDS versions had frequently cumulative intensity distributions that could be interpreted as twinning, i.e. the number of weak reflections was too small and the curves for the acentric reflections had a sigmoidal shape. This pheno

Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test

2008-02-22 Thread Clemens Vonrhein
Hi Uli, On Fri, Feb 22, 2008 at 09:53:36AM +0100, Ulrich Baumann wrote: > It is a known feature that data sets integrated with previous XDS versions > had frequently cumulative intensity distributions that could be > interpreted as twinning, i.e. the number of weak reflections was too small

Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test

2008-02-22 Thread Clemens Vonrhein
Hi Kay, On Fri, Feb 22, 2008 at 10:18:26AM +0100, Kay Diederichs wrote: > >By the way, I think a part of the problem may also arise that CORRECT or > >XSCALE apply too many correction factors -- try CORRECTIONS=DECAY only. > >Gives worse R-factors and worse I/sig(I) but sometimes nicer intesity

Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test

2008-02-22 Thread Tim Gruene
On Fri, 22 Feb 2008, Ulrich Baumann wrote: Or use pointless on the INTEGRATE.HKL file (not XDS_ASCII.HKL) and then SCALA -- we had one SAD case where this aided structure solution significantly, just beware that the unit cell is not postrefined by the CORRECT step then. I usually iterate the

Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test

2008-02-22 Thread Kay Diederichs
Hi Clemens, Clemens Vonrhein schrieb: Hi Kay, On Fri, Feb 22, 2008 at 10:18:26AM +0100, Kay Diederichs wrote: By the way, I think a part of the problem may also arise that CORRECT or XSCALE apply too many correction factors -- try CORRECTIONS=DECAY only. Gives worse R-factors and worse I/sig(

[ccp4bb]

2008-02-22 Thread Jordi Benach
Dear all, For those interested (companies), we have just published the invitation to tender for the diffractometer and the automated sample changer for the macromolecular crystallography beamline at Alba (Barcelona, Spain). See the relevant documentation in: http://www.cells.es/Industry/Tenders

[ccp4bb] XDS & pointless

2008-02-22 Thread Phil Evans
Since there has been mention of putting data from XDS into Pointless, I should say that I have made yet another (!) fix today for reading XDS data. It now flags & ignores reflections marked as MISFITS in the XDS file (marked with SD < 0). Previous versions included these reflections which a

[ccp4bb] http://packages.ubuntu.com/source/hardy/gpp4

2008-02-22 Thread Morten Kjeldgaard
Several packages useful for crystallographic computing and software   development will be available in Ubuntu Universe for the next release   of Ubuntu Linux 8.04 "Hardy Heron", to be officially released in April. - gpp4: library for CCP4 compatible programs (1.0.4): http://packages.ubuntu.com/so

[ccp4bb] Citations in supplementary information are invisible

2008-02-22 Thread William Scott
Hi Citizenry: This is worth reading: http://www.nature.com/nature/journal/v451/n7181/full/451887d.html Without knowingly doing so, I've short-cited coot and probably other crystallographic software in this way. I hope one day to redeem myself. Bill

[ccp4bb] binding of Au or Pt by serine

2008-02-22 Thread Mark J. van Raaij
Dear all, I would like to ask for examples of binding of Au or Pt by serines. The heavy atom databank does not give any hits, but we have a peptide which binds these metals and the only likely residue too bind them is serine (unfortunately I can't divulge its sequence...). Greetings, Mark M

Re: [ccp4bb] Citations in supplementary information are invisible

2008-02-22 Thread Warren DeLano
That's okay, we forgive you. As penance, you shall establish a new unsocial networking site: "myreciprocalspace.com" with your slighted colleagues cited as key crystal contacts obscured in the published unit sell. > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED

Re: [ccp4bb] Citations in supplementary information are invisible

2008-02-22 Thread Ethan Merritt
On Friday 22 February 2008 08:11, William Scott wrote: > Hi Citizenry: > > This is worth reading: > > http://www.nature.com/nature/journal/v451/n7181/full/451887d.html > > Without knowingly doing so, I've short-cited coot and probably other > crystallographic software in this way. I hope one >

[ccp4bb] New higher-throughput server for TLSMD analysis

2008-02-22 Thread Ethan Merritt
%% New higher-throughput server for TLSMD analysis %% http://skuld.bmsc.washington.edu/~tlsmd We have upgraded the TLSMD web server, and invite you all to try it out. The new server is faster, and can handle multiple jobs in parallel. It does additional pre-screening of sub

[ccp4bb] running fedora on virual PC 2007 (was RE: [ccp4bb] Vista)

2008-02-22 Thread Flip Hoedemaeker
Thanks to all for responding. In the end I found this blog that describes in detail how to do this, for the few of you who might be interested :) http://blogs.technet.com/seanearp/archive/2007/11/13/fedora-8-werewolf-on-vi rtual-pc-2007.aspx Flip -Original Message- From: CCP4 bulletin

Re: [ccp4bb] Citations in supplementary information are invisible

2008-02-22 Thread Warren DeLano
On a more serious note: with programs and databases, there are ways for authors to measure and justify their impact in the eyes of the funding agencies. For example, both the VMD and APBS projects track registrations and downloads so that they have documented usage statistics when it comes time t

Re: [ccp4bb] Vista

2008-02-22 Thread Deena Oren
Ok, OK, I get it. OSX or linux, though one response came in positively for the Vista. I will go to the Geek Store in NYC and have them convince me. I have been a mac person in the past as well as linux, but my mac laptop had some many hardware problems in its last year I had to hit the screen t