[ccp4bb] Spacegroup choices, reindexing and so on

Hi All, A user question about the xia2 behaviour has opened a pot of worms, and I thought I would ask the community for opinions. If (for example) you are using an automated data processing or analysis tool, and the systematic absences suggest a spacegroup choice, what would you like to do: (1)

Re: [ccp4bb] difference between I over sigma_I and I over sd

Hi Lu Yongzhi, It has to be said it is not obvious. However, there are as far as I can see at least three possible definitions of I/sigma, so here we go: (1) I/sigma (calculated, corrected perhaps) for individual observations - sigma based on counting statistics (2) Mean(I) / Sigma(mean) -

Re: [ccp4bb] Spacegroup choices, reindexing and so on

Dear Graeme, here is what I would do, or what I would like to have. If you are able to identify the Laue group of the data with some degree of certainty, then all of the processing and scaling should be carried out in this Laue group. Then, by looking at systematic absences you may give

Re: [ccp4bb] difference between I over sigma_I and I over sd

Dear all, speaking of I/sigma(I) when you use scalepack, how do you estimate it ? nathalie -- Dr. Nathalie Colloc'h, PhD CI-NAPS, UMR 6232 - UCBN - CNRS GIP Cyceron Bd Becquerel, BP5229 14074 Caen cedex FRANCE Tel. 33.2.31.47.01.32 Fax. 33.2.31.47.02.22 [EMAIL PROTECTED]

[ccp4bb] Swiss Light Source - Beamline Scientist Position

** We are looking for a Beamline Scientist for the Swiss Light Source * * The Paul Scherrer Institut is a centre for multi-disciplinary research and one of the world’s leading user laboratories. With its 1200 employees it belongs as an autonomous institution to the Swiss ETH domain and

Re: [ccp4bb] Spacegroup choices, reindexing and so on

Hi Manfred I agree with everything you say except the last bit about re-indexing! For those space groups with alternate settings, e.g. those with standard names C2 or P2221 or P21212, why is it necessary to re-index to the 'standard setting' when the data will have been already indexed

Re: [ccp4bb] Spacegroup choices, reindexing and so on

Dear Ian, I thought that in cases of for instance P-orthorhombic where you can have a screw axis along a, b, or c or any combination of it, the standard is always to make the unique axis the c-axis. I.e. the longest axis in P222, and P2(1)2(1)2(1), but the 2(1)-axis in P222(1) or P2(1)22 or

Re: [ccp4bb] difference between I over sigma_I and I over sd

LLI agree the difference between sd and SigI are a bit obscure. One referes to the spread of values about your mean I (The Sd of the reflection distribution) SigI is derived from the SIGI values estimated by the integration. There is some description in the CCP4 study weekend article by Phil Evans

[ccp4bb] Announcement - EMBO World Lecture Course

EMBO World Lecture Course on RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY We would like to announce an EMBO World Lecture Course on RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY, which will take place from Nov 09-14, 2008 in the town in Pune in India, on the

Re: [ccp4bb] Spacegroup choices, reindexing and so on

I meant to post this response to Pietro's reply to the BB: I agree that bugs in software are an ever-present source of annoyance, but the only software in general use that I'm aware of that can't cope with the conventional ITC-A settings is Arp/Warp (and even this was definitely true only for the

[ccp4bb] Crystal Imaging Systems - possibilities and recommendations

Dear Colleagues, We are currently contemplating the acquisition of an automated imaging system for crystallization screen plates (96-well). I am aware that Molecular Dimensions sells these systems ranging in price between 47 and 71 k€ and I am inviting your opinions, comments and advice on

Re: [ccp4bb] Spacegroup choices, reindexing and so on

On Jan 21, 2008, at 14:08, Ian Tickle wrote: I meant to post this response to Pietro's reply to the BB: I agree that bugs in software are an ever-present source of annoyance, but the only software in general use that I'm aware of that can't cope with the conventional ITC-A settings is Arp/Warp

[ccp4bb] Dual Head Stereo On FireGL

Hello all, I have 2 21inch CRTs connected to a stereo capable firegl card and I am hoping to enable the active stereo on the extended desktop. Stereo works on a single screen setup but does not on the extended desktop on 2 monitors. I have a similar setup on an nvidia quadro card using xinerama

[ccp4bb] SUMMARY: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5

Dear All, Thanks to Bill Scott, James Stroud and Jürgen Bosch for their responses. Here is the original email: We have recently bought a few iMacs for crystallography. I'm not keen on the supplied mighty mouse so I have switched to using a microsoft 3-button wheel

[ccp4bb] Help Superposition programmes!

Dear CCP4-programmers, I have recently installed CCP4 6.0.2 on a Mac G5 running (still) under OS 10.4. So far it was running OK - until tonight. When using superposition programmes (TOPP or Superpose) via the CCP4i I get the following message: Information from CCP4Interface script

Re: [ccp4bb] Help Superposition programmes!

Yes - you are right! It doesnt work on my PC either.. I dont understand the code at all. Did it work on an older version of CCP4? Eleanor Anita Bentley wrote: Dear CCP4-programmers, I have recently installed CCP4 6.0.2 on a Mac G5 running (still) under OS 10.4. So far it was running OK -

Re: [ccp4bb] Help Superposition programmes!

On Mon, Jan 21, 2008 at 06:28:58PM +0100, Anita Bentley wrote: I have recently installed CCP4 6.0.2 on a Mac G5 running (still) under OS 10.4. So far it was running OK - until tonight. When using superposition programmes (TOPP or Superpose) via the CCP4i I get the following message:

Re: [ccp4bb] Crystal Imaging Systems - possibilities and recommendations

Do you want an imager, or a more sophisticated system that will store plates and image them according to a schedule? With imaging, it is important to think about what you want out of the system, as it is easy to be disappointed with them. The images you get will not be as good as what you

[ccp4bb] CCP4 for bioinformatics?

Dear Crystallographers, Does anyone know of a bioinformatics counterpart of ccp4? It seems like there should really be such an entity, so that folks would not have to write scripts, reinventing the wheel all of the time. I am trying right now to manipulate some sequences into various forms,

Re: [ccp4bb] CCP4 for bioinformatics?

On Monday 21 January 2008 15:33, Jacob Keller wrote: Dear Crystallographers, Does anyone know of a bioinformatics counterpart of ccp4? It seems like there should really be such an entity, so that folks would not have to write scripts, reinventing the wheel all of the time. I am trying

Re: [ccp4bb] CCP4 for bioinformatics?

manipulate some sequences into various forms, and I was imagining a moleman homolog for bioinformatics (perhaps seqman?). as a matter of fact, i did write exactly that program nine years ago - http://xray.bmc.uu.se/usf/seqman_man.html :-) - not quite a 'ccp4 for bioinformatics' but indeed

[ccp4bb] protein expression problem

Hi, I have been trying to express a rat protein in bacteria. The MBP-fusion expressed at very high level (~ 40 mg/L) while the GST-fusion and His-tag only gave inclusion bodies. The problem is that all protein runs in the void volume on a size-exclusion column (s-200, hepes, pH 7.4, 200

Re: [ccp4bb] protein expression problem

Hi Chen, You could try adding some detergent or other solubilising agent (eg NDSBs) to your buffer. Have you tried other pHs? If you are sat near to or on the pI of your protein, it will be at its least soluble and more likely to aggregate. I've had protein behave like yours at pH 7.5 but behave

Re: [ccp4bb] CCP4 for bioinformatics?

BioPython There is also BioPerl And BioJava too, http://biojava.org/wiki/Main_Page Depend of your computing preference, and the size of your project... Regards, -- Watier Yves PhD Student, European Synchrotron Radiation Facility (ESRF) Experiments Division / Materials Science Group ID31