Re: [ccp4bb] mosflm gain

2011-03-04 Thread A Leslie
Dear Bryan, The quick answer is no. As David Waterman mentioned, it has a default value for the gain for each type of detector that it can deal with. A more detailed answer. An incorrect value for the gain can be indicated by values of the BGRATIO which differ

Re: [ccp4bb] mosflm gain

2011-03-04 Thread A Leslie
Dear All, spotted a mistake in my response, please see the correction below (in bold): There are a host of caveats in this procedure. For example, if the images contains significant diffuse scatter around the Bragg spots, the BGRATIO may be above 1.0 ... this is probably the commonest

Re: [ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of 3.0 rule]

2011-03-04 Thread Kay Diederichs
Maia, provided radiation damage is not a major detrimental factor, your data are just fine, and useful also in the high resolution shell (which still has I/sigma of 2.84 so you could probably process a bit beyond 2.25A). There is nothing wrong with R_meas of 147.1% since, as others have

Re: [ccp4bb] I/sigmaI of 3.0 rule

2011-03-04 Thread John R Helliwell
Dear Roberto, Overnight I recall an additional point:- In chemical crystallography, where standard uncertainties are routinely avaliable for the molecular model from the full matrix inversion in the model refinement, it is of course possible to keep extending your resolution until your bond

[ccp4bb] cooled incubator for crystallisation plates

2011-03-04 Thread Hough, Michael A
Hi, Could anyone recommend a reasonably priced (i.e. less than £3000) cooled incubator for crystallisation plates? We plan to initially use this at 4C but flexibility would be useful. One that we have considered is the LEEC LT2J

[ccp4bb] PhD studentships for October 2011: University of Essex

2011-03-04 Thread Hough, Michael A
Applications are invited for 3 year PhD studentships in my lab, available for October 2011 in the Department of Biological Sciences at the University of Essex, Colchester. The studentship titles are: Defining the structural factors that control ligand discrimination in haemoproteins Using

Re: [ccp4bb] I/sigmaI of 3.0 rule

2011-03-04 Thread Roberto Battistutta
Dear all, just to say that I really appreciate and thank the many people who spent time responding to my issue. I have read with much interest (and sometimes with fun) all comments and suggestions, very interesting and useful. Thanks a lot, Bye, Roberto. Roberto Battistutta Associate Professor

Re: [ccp4bb] I/sigmaI of 3.0 rule

2011-03-04 Thread Phil Evans
This is very closely related to the way in which I would like to think about this: if you consider adding another thin shell of data, are you adding any significant information? Unfortunately as Garib Murshudov has pointed out, we don't have any reliable way of estimating the information

Re: [ccp4bb] I/sigmaI of 3.0 rule

2011-03-04 Thread Marjolein Thunnissen
hi Recently on a paper I submitted, it was the editor of the journal who wanted exactly the same thing. I never argued with the editor about this (should have maybe), but it could be one cause of the epidemic that Bart Hazes saw best regards Marjolein On Mar 3, 2011, at 12:29 PM,

Re: [ccp4bb] cooled incubator for crystallisation plates

2011-03-04 Thread Ed Pozharski
On Fri, 2011-03-04 at 10:39 +, Hough, Michael A wrote: Could anyone recommend a reasonably priced (i.e. less than £3000) cooled incubator for crystallisation plates? Consider wine coolers - many thermoelectric (vibration-free) models are available. Normally they don't go down to 4 degrees

Re: [ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of 3.0 rule]

2011-03-04 Thread Maia Cherney
Kay, Thank you for your explanation. The radiation damage was not the factor, but there was something strange about this crystal (actually two crystals had the same strange behavior). I could not process them in HKL2000, but it showed the problem (see pictures in the attachment). The

[ccp4bb] bit off topic

2011-03-04 Thread Ariel Talavera
Hi CCP4ers, Is there any place from where I could download .pdb files of LPS lipid A from different bactiria? Thanks a lot in advanced. regards, Ariel

Re: [ccp4bb] weird crystals, I/sigma of 3.0 rule

2011-03-04 Thread Maia Cherney
Hi James, I remember that P1 did not help. That was like 2 years ago. That crystal was very important at that time, so I had to use it. There were many other crystals since then (native, mutants and complexes) in the same space group without problems. But also I had even a more weird crystal

[ccp4bb] XSCALE vs scala

2011-03-04 Thread José Trincão
Hello all, I've been converting my XDS files (XDS_ASCII.hkl) to mtz using pointless and then running scala to get the work mtz. I like this procedure because I get useful info, (such as Rpim), that I don't know how to get otherwise. I there any advantage/disadvantage of using this procedure

[ccp4bb] off topic: GPCR membane insertion/orientation

2011-03-04 Thread Justin Hall
Dear Community, In trying to trouble shoot an experiment I have become interested in the cellular process that regulates the insertion and proper orientation of membrane proteins. I am looking for references for how a GPCR is correctly oriented during expression (i.e. the extra cellular

Re: [ccp4bb] off topic: GPCR membane insertion/orientation

2011-03-04 Thread Van Den Berg, Bert
Hi Justin, I'm not sure if there are papers regarding this for GPCRs, but the phenomenon you're referring to is the positive inside rule. This basically means that the SecY translocon (in a way that is only partially clear) mediates membrane protein insertion in such a way that the (net)

Re: [ccp4bb] off topic: GPCR membane insertion/orientation

2011-03-04 Thread Pascal Egea
Hi Justin, Since GPCRs are polytopic a-helical transmembrane proteins, it is very likely that (1) insertion into the membrane is primarily performed by the Sec61 complex AKA translocon and (2) targeting to the membrane would be controlled by the signal recongition particle and its receptor. the

Re: [ccp4bb] off topic: GPCR membane insertion/orientation

2011-03-04 Thread Daniel Picot
In addition to Bert remarks, you can read this paper from the positive inside rule instigators. Seppälä S, Slusky JS, Lloris-Garcerá P, Rapp M, von Heijne G. Control of membrane protein topology by a single C-terminal residue. Science. 2010 Jun 25;328(5986):1698-700. Epub 2010 May 27. PubMed

[ccp4bb] Fwd: [ccp4bb] XSCALE vs scala

2011-03-04 Thread José Trincão
Begin forwarded message: From: Graeme Winter graeme.win...@googlemail.com Date: March 4, 2011 4/3/11 - 4:51 To: José Trincão trin...@dq.fct.unl.pt Subject: Re: [ccp4bb] XSCALE vs scala Hi Jose, if you are following the usual XDS procedure, the data will have already been scaled by the XDS

Re: [ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of 3.0 rule]

2011-03-04 Thread Kay Diederichs
Am 04.03.2011 11:11, schrieb Kay Diederichs: There is nothing wrong with R_meas of 147.1% since, as others have said, R_meas is not limited to 59% (or similar) as a refinement R-factor is. Rather, R_meas is computed from a formula that has a denominator which in the asymptotic limit (noise)

[ccp4bb] merge datasets

2011-03-04 Thread Florian Schmitzberger
Dear All, I have two questions: 1) I have collected multiple, native datasets (5) from the same crystal (different parts of the crystals exposed with different transmission and oscillation angles). Each dataset on its own is close to complete (96-98 %). Naturally, differences in exposure,

Re: [ccp4bb] mosflm gain

2011-03-04 Thread James Holton
I have found that the best way to get the GAIN right in MOSFLM is to have a look at the optimum Sdfac parameter at the end of SCALA (the first of the three SDCORRection values). Specifically, if SDFac is 1, then you need to increase the GAIN. This is because SDFac1 means that the spots were

Re: [ccp4bb] I/sigmaI of 3.0 rule

2011-03-04 Thread Roberto Battistutta
Dear Phil, I completely agree with you, your words seem to me the best philosophical outcome of the discussion and indicate the right perspective to tackle this topic. In particular you write In the end, the important question as ever is does the experimental data support the conclusions drawn

[ccp4bb] Post Doc position in Molecular biology

2011-03-04 Thread Preben Morth
Dear ccp4bb On behalf of Professor Geir Christensen I would like to draw your attention to a post position in molecular biology http://uio.easycruit.com/vacancy/519990/70331?iso=no Please contact Geir Christensen for further information J. Preben Morth, Ph.D Group Leader Membrane Transport

[ccp4bb] off-topic replay: glycerol in protein stock solutions

2011-03-04 Thread Brett, Thomas
Hi guys: I know this has been asked before, but I want to get (current) opinions and observations once again. Every once in a while, you work with a protein that needs to have a little something added to the buffer to keep it soluble. The most common trick is addition of glycerol (usually

Re: [ccp4bb] off-topic replay: glycerol in protein stock solutions

2011-03-04 Thread Van Den Berg, Bert
Hi Tom, Adding glycerol to (crystallization) buffers is a very common practice when working with membrane proteins. Many membrane proteins have been crystallized (perhaps even the majority) with glycerol, even up to 30% v/v. So, at least for membrane proteins, there is no problem. Bert On