Re: [ccp4bb] Highest shell standards

2007-03-22 Thread Eleanor Dodson
I feel that is rather severe for ML refinement - sometimes for instance it helps to use all the data from the images, integrating right into the corners, thus getting a very incomplete set for the highest resolution shell. But for exptl phasing it does not help to have many many weak reflectio

[ccp4bb] iMosflm 0.5.2 available now

2007-03-22 Thread Harry Powell
Hi folks The latest release of iMosflm (the new Mosflm GUI) is available now. The major development is a native MS-Windows version. Beta-testing indicates that this is at least as reliable as the other versions. For further details, including those for download and installation, see: ht

Re: [ccp4bb] Scale factor in ccp4

2007-03-22 Thread Eleanor Dodson
When youu run scalepack2mtz the GUI always follows this by TRUNCATE to convert Is to Fs At that stage there is an attempt to put the data on roughly an absolute scale, either using the NRES you gave as input or if that is not set, I think assuming 50% of the cell volume is protein. Anyway the

Re: [ccp4bb] Scale factor in ccp4

2007-03-22 Thread Johan Turkenburg
Hi, You can read both files back into scalepack and scale them. Better still, if you have the .x files from denzo, read both sets into scalepack. Scenarios both in the manual. Johan yang li wrote: Hi: I have two set of data from the same crystal with the names 1.sca and 2.sca, they hav

Re: [ccp4bb] Scale factor in ccp4

2007-03-22 Thread George M. Sheldrick
A less convoluted method is to read both .sca files into xprep, scale them together and write out the combined .sca file. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-5

[ccp4bb] Workshop: Macromolecular Crystallography at PETRA III

2007-03-22 Thread Michele Cianci
Beamline Design Workshop Macromolecular Crystallography at PETRA III EMBL-Hamburg Outstation, April 23 to 25, 2007 Starting in 2007, the PETRA storage ring in Hamburg, Germany, will be converted into a 3rd generation source for synchrotron radiation. The new PETRA III storage ring

Re: [ccp4bb] Scale factor in ccp4

2007-03-22 Thread Eleanor Dodson
Yes - and actually Johan's suggestion is the best - one should not merge two sets of already merged data, better is to scale and merge all together in scalepack.. Eleanor George M. Sheldrick wrote: A less convoluted method is to read both .sca files into xprep, scale them together and write o

Re: [ccp4bb] Highest shell standards

2007-03-22 Thread Ranvir Singh
I will agree with Ulrich. Even at 3.0 A, it is possible to have a structure with reasonable accuracy which can explain the biological function/ or is consistent with available biochemical data. Ranvir --- Ulrich Genick <[EMAIL PROTECTED]> wrote: > Here are my 2-3 cents worth on the topic: > > Th

Re: [ccp4bb] Highest shell standards

2007-03-22 Thread Santarsiero, Bernard D.
There are journals that have specific specifications for these parameters, so it matters where you publish. I've seen restrictions that the highest resolution shell has to have I/sig > 2 and completeness > 90%. Your mileage may vary. I typically process my data to a maximum I/sig near 1, and compl

[ccp4bb] EMBO Workshop on THE CHEMISTRY AND BIOCHEMISTRY OF CATALYSIS BY BIOLOGICAL SYSTEMS

2007-03-22 Thread Andrea Schmidt
A programme is now available for the EMBO Workshop on THE CHEMISTRY AND BIOCHEMISTRY OF CATALYSIS BY BIOLOGICAL SYSTEMS - 20 - 22 June 2007, EMBL Hamburg Please visit our website for workshop and registration details: http://www.embl-hamburg.de/workshops/2007/catalysis/ or contact: [EMAIL PRO

Re: [ccp4bb] Highest shell standards

2007-03-22 Thread Sue Roberts
I have a question about how the experimental sigmas are affected when one includes resolution shells containing mostly unobserved reflections. Does this vary with the data reduction software being used? One thing I've noticed when scaling data (this with d*trek (Crystal Clear) since it's

Re: [ccp4bb] Highest shell standards

2007-03-22 Thread Petrus H Zwart
> I typically process my data to a maximum I/sig near 1, and > completeness in > the highest resolution shell to 50% or greater. It What about maps computed of very incomplete datasets at high resolution? Don't you get a false sense of details when the missing reflections are filled in with DFc

[ccp4bb] Postdoc and Ph.D. student positions

2007-03-22 Thread Clemens Steegborn
Postdoctoral Position in Structural Biology / Biochemistry We are looking for a highly motivated Postdoc for our laboratory at the Institute for Physiological Chemistry at Ruhr-University Bochum, Germany. Our work involves biochemical and structural studies on cellular signaling systems with

Re: [ccp4bb] Highest shell standards

2007-03-22 Thread Jose Antonio Cuesta-Seijo
I have observed something similar myself using Saint in a Bruker Smart6K detector and using denzo in lab and syncrotron detectors. First the I over sigma never really drops to zero, no mater how much over your real resolution limit you integrate. Second, if I integrate to the visual resolution

Re: [ccp4bb] Highest shell standards

2007-03-22 Thread Santarsiero, Bernard D.
My guess is that the integration is roughly the same, unless the profiles are really poorly defined, but that the scaling that is suffering from using a lot of high-resolution weak data. We've integrated data to say I/sig = 0.5, and sometimes seem more problems with scaling. I then cut back to I/si

[ccp4bb] X-ray generator uninterruptible power supply

2007-03-22 Thread William Scott
Hi Citizens: Does anyone use an uninterruptible power supply for their X-ray generator? Here at UCDIY, the electricity supply is pretty sketchy, and it is hammering our X-ray generator every time someone forgets to feed the hamster or grease his wheel. If so, how much does such a thing c

Re: [ccp4bb] X-ray generator uninterruptible power supply

2007-03-22 Thread Santarsiero, Bernard D.
On Thu, March 22, 2007 3:46 pm, William Scott wrote: > Hi Citizens: > > Does anyone use an uninterruptible power supply for their X-ray > generator? Here at UCDIY, the electricity supply is pretty sketchy, > and it is hammering our X-ray generator every time someone forgets to > feed the hamster o

[ccp4bb] How to subtract one electron density map from another

2007-03-22 Thread Qing Xie
Hi, I'm trying to get the difference map by subtracting the native electron density map from the complex electron density map. MAPMASK has a function of ADD/MULT, but I don't know how to use it? Any other ways to attack this problem in real space? Thanks in advance, Qing

Re: [ccp4bb] How to subtract one electron density map from another

2007-03-22 Thread Paul Emsley
On Thu, 2007-03-22 at 16:06 -0500, Qing Xie wrote: > I'm trying to get the difference map by subtracting the native electron > density map from the complex electron density map. MAPMASK has a function > of ADD/MULT, but I don't know how to use it? > Any other ways to attack this problem in real s

Re: [ccp4bb] X-ray generator uninterruptible power supply

2007-03-22 Thread Matthew . Franklin
CCP4 bulletin board wrote on 03/22/2007 04:46:35 PM: > Hi Citizens: > > Does anyone use an uninterruptible power supply for their X-ray > generator? Here at UCDIY, the electricity supply is pretty sketchy, > and it is hammering our X-ray generator every time someone forgets to > feed the hamster

Re: [ccp4bb] X-ray generator uninterruptible power supply

2007-03-22 Thread Robert Sweet
Frankly, Bill, this is what you need: http://ce.eng.usf.edu/pharos/wonders/Modern/itaipu.html Yours, Bob On Thu, 22 Mar 2007, [EMAIL PROTECTED] wrote: CCP4 bulletin board wrote on 03/22/2007 04:46:35 PM: Hi Citizens: Does anyone use an uninterruptible power supply for their X-ray genera

Re: [ccp4bb] X-ray generator uninterruptible power supply

2007-03-22 Thread David J. Schuller
On Thu, 2007-03-22 at 18:54 -0400, [EMAIL PROTECTED] wrote: > I never considered getting a UPS for my generator, even though our building > has no backup power and Con Ed also forgets to feed their hamsters > occasionally. What I did get was a UPS for my cryostream - I figured that > the data col

Re: [ccp4bb] How to subtract one electron density map from another

2007-03-22 Thread Ulrich Genick
Why not simply scale the two data sets, and subtract corresponding Fs from one another and then calculate a map from those Fs. If you want to an error-weighted map, you should also perform error propagation on your sigF. Assuming that the two errors are independent of one another the formula

Re: [ccp4bb] How to subtract one electron density map from another

2007-03-22 Thread Edward A. Berry
Mapman (Uppsala software factory) allows you to subtract maps if they are on the same grid. You may need to multiply one map by a factor (again in mapman) to make the background flat in the regions you believe to be identical. Linearity of the Fourier Transform implies you could get the same resu