Re: [ccp4bb] Confusion about space group nomenclature

2014-04-30 Thread Ian Tickle
> On Tue, 2014-04-29 at 16:12 +0200, Bernhard Rupp wrote: > > > Response to off-board mail: > > > > > > >How about [calling them] non-centro-symmetric space groups, as I > often tell my students? > > > > > > Almost, but not exact enough. > > > > > > The 65 are only a subset of non-centrosymmet

Re: [ccp4bb] shelxCDE in ccp4i

2014-04-30 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mirek, can you check shelx c/d/e are actually in your path when you start ccp4i? You can open a terminal and type 'shelxc' to check and then start ccp4i from the very same terminal - are shelx c/d/e still greyed out? Best, Tim On 04/30/2014 01:

[ccp4bb] activation of ShelxC/D/E

2014-04-30 Thread Shanti Pal Gangwar
Dear All I am facing problem in installation of ShelxCDE on CCP4 6.4.0. I have installed CCP4 and all the programs are running successfully. I copied and pasted ShelxCDE executables into CCP4 bin. Earlier also I adopted the same procedure to activate ShelxCDE on CCp4 interface and it worked. But

Re: [ccp4bb] activation of ShelxC/D/E

2014-04-30 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Shanti Pal, when you download the shelx binaries the executable flag is not necessarily set. Can you check with 'ls -l $CBIN/shelxc' if this is the case? You can set it with 'chmod +x $CBIN/shelxc'. Best, Tim On 04/30/2014 11:51 AM, Shanti Pal

[ccp4bb] metals disapear

2014-04-30 Thread Dean Derbyshire
Hi all, Has anyone experienced catalytic metal ions disappearing during data collection ? If so, is there a way of preventing it? D. Dean Derbyshire Senior Research Scientist [cid:image001.jpg@01CF6470.5FA976D0] Box 1086 SE-141 22 Huddinge SWEDEN Visit: Lunastigen 7 Direct: +

Re: [ccp4bb] metals disapear

2014-04-30 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Dean, this is probably a very common observation: X-rays produce reducing electrons and as you reduce a metal I imagine it does not like its chemical environment as much as it did highly charged. Everything you can do to avoid radiation damage s

[ccp4bb] anomalous signal

2014-04-30 Thread Faisal Tarique
Dear all I am working on a metalloprotein which probably contains Ca at its active site..The sulfur containing amino acid constitutes almost 5.4% of the total amino acid residues of this protein..I have collected the data at home source (CuKalpha=1.54A)..Since f'' of Sulfur is 0.56 and that of Ca

Re: [ccp4bb] metals disapear

2014-04-30 Thread Andrew Leslie
Can the radiation damage gurus comment on this ? I know there is a problem with radiation damage changing the valence state of metals, but I don't remember hearing about the metal actually being lost due to radiation damage. Is this really common ? Thanks, Andrew On 30 Apr 2014, at 11:46, Tim

Re: [ccp4bb] anomalous signal

2014-04-30 Thread Tobias Weinert
Dear Faisal, you could use Phenix to do an f’’ refinement against the data like described here: Liu, Q., Liu, Q. & Hendrickson, W. A. (2013). Acta Cryst. D69, 1314-1332. best regards, Tobias On 30 Apr 2014, at 14:01, Faisal Tarique wrote: > Dear all > > I am working on a metalloprotein w

Re: [ccp4bb] metals disapear

2014-04-30 Thread Keller, Jacob
Attenuate the beam and take many more frames such that you get a full dataset, albeit at slightly lower resolution, before the metals go away. In other words, reduce dose/degPhi. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dean Derbyshire Sent: Wednesday, April 30

[ccp4bb] Pilatus and Strategy wrt Radiation Damage

2014-04-30 Thread Keller, Jacob
Dear Pilatus/Radiation Damage Cognoscenti, I read a few years ago, before the advent of Pilatus detectors, that the best strategy was a sort of compromise between number of images and detector readout noise "overhead." I have heard that Pilatus detectors, however, have essentially no readout no

Re: [ccp4bb] metals disapear

2014-04-30 Thread Gerard Bricogne
Dear Dean (and Andrew), I am certainly no radiation damage guru, but at the RD8 Workshop in Hamburg 3 weeks ago (http://www.rd-eight.org/RD8-01/) I heard a talk by Pernille Harris about the photoreduction by X-rays of Cu(II) to Cu(I) in a Cu-insulin crystal. Tim's description couldn't b

Re: [ccp4bb] Pilatus and Strategy wrt Radiation Damage

2014-04-30 Thread Sanishvili, Ruslan
Hi Jacob, I'll take a first crack as I am sure many will follow. It is true that with CCD detectors one has to be careful how small an oscillation range to use for a frame before read noise starts to eat into the data quality. Pilatus offers two major new features - is fast and is photon counti

Re: [ccp4bb] metals disapear

2014-04-30 Thread Zbyszek Otwinowski
My comments: Such observation is very uncommon for metals involved in catalysis by proteins. I have seen quite a few such structures involving Mg, Ca, Fe, Mn, Zn and most of the radiation damage was not at the catalytic metal. In case of Fe once I noticed slight shift in the position of the Fe ion

Re: [ccp4bb] anomalous signal

2014-04-30 Thread Eleanor Dodson
Well - this is pretty common, and really doesnt matter. I just let SHELXC/D give an "occupancy" to its anom scatterer solutions and assume that the stronger one is Ca. But in fact it wont matter at all for the phasing, and IF the experiment works it is easy to sort out S from Ca in the final map.

Re: [ccp4bb] metals disapear

2014-04-30 Thread Sanishvili, Ruslan
Dear Dean, You have already received excellent insight into radiation effects on metals. From personal experience, it doesn't take long for the metal occupancy to go down to 80%. Of course it is not anywhere near "disappearing" but then again, we don't know the details of your data collection a

Re: [ccp4bb] anomalous signal

2014-04-30 Thread Jim Pflugrath
The anomalous signal will always come from both Ca and S and any other atoms in the crystal. One can determine whether an anomalous difference Fourier peak is from a sulfur on a cysteine, methionine from the model, right? As for whether a peak that is not part of an amino acid id Ca++ or Sulfu

Re: [ccp4bb] metals disapear

2014-04-30 Thread Zbyszek Otwinowski
If metal ion will be sensitive to radiation depends on its redox chemistry and not its X-ray properties. For a metal to be affected by radiation dose it needs to be reduced by free radicals. However, such metals are rarely (by gene counts or deposits in PDB) present in catalytic sites of enzymes. T

Re: [ccp4bb] Pilatus and Strategy wrt Radiation Damage

2014-04-30 Thread Harry Powell
Hi Marcus Mueller (from Dectris, who develop and manufacture the Pilatus) did some work on this a couple of years ago and determined that an oscillation angle ~ 0.5x the mosaicity of the crystal (using the XDS value of mosaicity, which is not the same as Mosflm's); the abstract says - T

[ccp4bb] NWCW 2014: Last day to register at early registration rates

2014-04-30 Thread Dale Tronrud
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Northwest Crystallography Workshop http://oregonstate.edu/conferences/event/nwcw2014/ June 20-22, 2014 The (Pacific) Northwest Crystallography Workshop is a regional gathering of people who are interested

Re: [ccp4bb] anomalous signal

2014-04-30 Thread Tobias Weinert
@ Jim Me neither, i should read before i reply, my fault. Tobias On 30 Apr 2014, at 17:15, Jim Pflugrath wrote: > The anomalous signal will always come from both Ca and S and any other atoms > in the crystal. One can determine whether an anomalous difference Fourier > peak is from a sulfu

Re: [ccp4bb] anomalous signal

2014-04-30 Thread Keller, Jacob
I myself have never seen a separate peak that was a single sulfur atom. I've seen, in a moderately-radiation-damaged dataset, little shards of anomalous scattering density in Phaser-generated LLG maps. They were in the interior of the protein, and the closest possible atoms were sulfurs. They w

Re: [ccp4bb] metals disapear

2014-04-30 Thread Jrh Gmail
Dear Dean An example, albeit not a metal, can be found here:- http://journals.iucr.org/s/issues/2007/01/00/xh5011/xh5011.pdf Such specific damage has a long history:- http://www.sciencedirect.com/science/article/pii/0022024888903223 An X-ray sensitive metals centre is the Mn5Ca OEC of PS II and d

Re: [ccp4bb] metals disapear

2014-04-30 Thread Sanishvili, Ruslan
>The question about metal sensitivity to radiation cannot be answered in >general; it needs to be discussed in specific chemical coordination >context. Agreed. The author of the original question should have provided more details about the metal in question, about the samples and the way experime

Re: [ccp4bb] metals disapear

2014-04-30 Thread Felix Frolow
Are these metals there in the beginning to experiment before radiation damage “destroy” them? Easy to check if X-ray fluorescence facility is installed on the beam line you are measuring. It is sensitive technique and we constantly use it in the beginning of every measurement. FF Dr Felix Frol