Re: [ccp4bb] rescuing crashing-out protein eluted from Nickel column

Thank you all for the quick replies - I'm trying many of the tips in small batches and would send out a feedback as soon as appropriate, gratefully, - J.J. On 2/14/08, Jacob Wong <[EMAIL PROTECTED]> wrote: > > Dear all, > > I just ran into this problem and would like to see if I could get some > h

Re: [ccp4bb] rescuing crashing-out protein eluted from Nickel column

JJ Dilute your fractions for this prep. Do gradient elution in the future. Again dilute the fractions immediately. Figure out a better buffer will be helpful. Cheers, Chun Luo, Ph.D. The Protein Expert Accelagen, Inc. 11585 Sorrento Valley Road, Suite 107 San Diego, CA 92121

[ccp4bb] rescuing crashing-out protein eluted from Nickel column

Dear all, I just ran into this problem and would like to see if I could get some helpful tips before my protein completely crashes out. I have a protein as 6His fusion and it remained bound to the Ni resin with 40 mM Imidazole wash (added to 1XPBS) but then was eluted off with 200 mM (added to 1XP

[ccp4bb] BCA/CCP4 Summer School on Macromolecular Crystallography XV

BCA/CCP4 Summer School XV Biochemistry Department and St. Edmund Hall, University of Oxford. 7th-12th September 2008. Scope. The BCA Summer School is a combined taught and practical course intended primarily for students and researchers new to crystallography. Its aim is to provide compre

Re: [ccp4bb] counting constraints?

The point where this restraint discussion regarding counting of restraints seems to become murky imho, is when it comes to 'independence' of restraints. Ok - say only active and independent restraints (AIRs) count in the determination of observation/parameter ratio, where observations includes d

Re: [ccp4bb] counting constraints?

Bart Yes, I think Peter's original question arose in the context of predicting Rfree. For that we have to consider the *total* restraint count separately from the total observation count, and provided each restraint is independent of all other restraints it counts as one, and similarly provided t

Re: [ccp4bb] counting constraints?

Thanks Ian, I saw experimental observations and restraints (empirical observations) as completely different but I now see they are just two different sources of information that restrain the model parameters. So when you are counting they can all get "one vote" as long as the observations are

Re: [ccp4bb] counting constraints?

Peter, Sorry I re-read your e-mail & realised you're asking a slightly different question from the one I answered. Of course you count the restraints in your structure, not the ones in the dictionary, so in the example you give there would be 4 not 1. Each bond, angle, torsion, VDW contact, B-fa

Re: [ccp4bb] counting constraints?

Peter, Bart Actually the restraint weight doesn't affect the restraint count one iota and as far as counting is concerned each restraint has exactly one 'vote' in the count. However there is an important proviso: the restraints must be completely independent to contribute fully to the count. Sup

[ccp4bb] ncs symmetry planes, and bias

I really enjoyed the recent discussion of ncs coupling and bias on ccp4bb, as usual. Although unlikely, the problem will be real in a significant number of cases. At this time there is sufficient computing power so that refinement calculations can be made with several different test sets. In t

Re: [ccp4bb] counting constraints?

Hi Pete, In your example it would count as 4 restraints, not constraints, and certainly not 4 observations or 4 parameters. It is not clear to me how to quantify the information content in restraints, it probably depends on the type of restraint and surely on the weight. Maybe information the

[ccp4bb] counting constraints?

Hi, The recent discussion on Rwork/Rfree ratio reminded me of something I was wondering about (*). When counting constraints as observations for determining the observation to parameter ratio, is each unique constraint counted, or each time a given constraint is used. For example, if there ar

Re: [ccp4bb] Strange SFALL error

About to leave for 6 weeks - but try expanding map to P1 and using that - SFALL only supports a limited set of spacegroups.. Eleanor Dirk Kostrewa wrote: Dear CCP4ers, I've created an artificial map in C2 with MAPMAN and made sure that the axis order and sampling is consistent with SFALL, wh

Re: [ccp4bb] first week of CCP4 community wiki

Would it be too much to ask that the person sending the summary email would also put that (or equivalent information) in the wiki? Esko Quoting Kay Diederichs <[EMAIL PROTECTED]>: > Andreas Förster schrieb: > > Hey Kay, > > > > I'm not even sure I see a problem with reposting. All ccp4 p

Re: [ccp4bb] first week of CCP4 community wiki

Andreas Förster schrieb: Hey Kay, I'm not even sure I see a problem with reposting. All ccp4 posts are archived, and the archive is public. So, by posting to the list, you're already implicitly consenting to having your comment made public. How is this different from being included in the

Re: [ccp4bb] first week of CCP4 community wiki

Hey Kay, I'm not even sure I see a problem with reposting. All ccp4 posts are archived, and the archive is public. So, by posting to the list, you're already implicitly consenting to having your comment made public. How is this different from being included in the wiki? That said, I think

[ccp4bb] Commonwealth Scholarships for MSc Structural Biology by Distance Learning

Dear all, For the second consecutive year, the School of Crystallography, Birkbeck College, University of London is offering scholarships in association with the Association of Commonwealth Universities. These scholarships offer 100% fee waivers on our web based MSc in Structural Biology by

[ccp4bb] Job opportunities: Helmholtz Department of Structural Biology, DESY Hamburg

W3-Professor for Structural Biology - Head of the Helmholtz Department of Structural Biology and a Junior (W1) Professorship Dear Colleagues, we are writing to inform you about exciting new job opportunities in a newly established, independent structural biology laboratory. We would appreciate if

Re: [ccp4bb] Summary of Thermofluor

mesters wrote: > Sorry for the off-topic but can somebody recommend highly a sensitive > RT-PCR machine for the thermofluor experiment (sypro orange). > That would imply excitation below 500 nm (ideally 470) and detection > at about 570 nm, right? I know several simple machines have a problem > wit

[ccp4bb] first week of CCP4 community wiki

Dear all, one week ago the CCP4 community wiki at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Main_Page was announced. I had to learn the meaning of the word "slashdotted" on that occasion (thanks Paul!). In the meantime there have been a total of 3,037 page views, and 250 p

[ccp4bb] Strange SFALL error

Dear CCP4ers, I've created an artificial map in C2 with MAPMAN and made sure that the axis order and sampling is consistent with SFALL, which I want to use for calculating structure factors from this map. However, SFALL (MODE SFCALC MAPIN) fails with the rather obscure error message: "SFA

Re: [ccp4bb] CCP4 maps into Turbo frodo

On Wednesday 13 February 2008 17:47:34 Laurent Maveyraud wrote: > I am trying to read a CCP4 electron density map into turbo_frodo, without > success. It seems that the mappage program that was distributed with > turbo_frodo does not work on our system (Linux Mandrake) : it produces a > segmentatio

[ccp4bb] Post Doctoral Fellowships (24 months)

Structural Studies on Human Proteins of Medical Relevance Karolinska Institutet, Structural Genomics Consortium Department of Medical Biochemistry and Biophysics Web link: http://sgc.ki.se/jobs.html Structural Biochemistry of Integral Membrane Proteins (2 positions) We seek two talented researche