[ccp4bb] PhD fellowship at the Faculty of Health and Medical Sciences, University of Copenhagen

PhD fellowship at the Faculty of Health and Medical Sciences, University of Copenhagen We are offering a three-year PhD fellowship within a project based upon positive allosteric modulation of kainate receptors (KARs). The employment as PhD fellow is full time and for 3 years. The PhD

[ccp4bb] B value analysis and validation tool

Dear All, Kindly be informed that new program for analysis and validation of macromolecular B values named ToBvalid is already available online. (https://github.com/ToBvalid/tobvalid) Please find the user guide here: https://github.com/ToBvalid/tobvalid/blob/master/doc/User_Guide.pdf Here is

Re: [ccp4bb] AW: [ccp4bb] Cold cabinet recommendations for AKTA Pure

Hi Alan, I think new AKTA collector can be refrigerated. If this is not an option, consider putting only collector in the cold cabinet and cooling down the buffers. Also, you can put only columns and fraction collector inside cabinet which has side port for such use. Although you will have to

Re: [ccp4bb] Ideas for improving refinement with anisotopic data.

Dear Matthew, You seem to have been unlucky with this data collection. STARANISO would be prepared to see significant data extending to 2.0A along a*, 2.7A along b*, and 1.7A along c*. The latter limit, however, involves some guess work via the fitting by an ellipsoid of a cut-off surface

[ccp4bb] AW: [ccp4bb] Cold cabinet recommendations for AKTA Pure

hi alan, why do you want to put the thing in a cold cabinet? if you have protease problems, there are better ways to get rid of them than exploiting Q10. on the other hand, you'll increase viscosity and thus slow down the flow rates. also, the high humidity will reduce the lifetime of your Äkta

Re: [ccp4bb] Cold cabinet recommendations for AKTA Pure

Hi Alan We got one a few years back, from Fisher, although I think Thermo are the manufacturer's: Refrigerator FRCR4504W Forma chromatography THERMO SCIENTIFIC FORMA FRCR4504W They also arranged for a heavy metal shelf to hold the AKTA as the normal shelves won't hold the weight. We only

Re: [ccp4bb] Ideas for improving refinement with anisotopic data.

*Please* dont throw good 1.8A data for the sake of statistics! You should see more detail along certain directions You will publish your structure providing honest details of the anisotropy (I hope..) but it is the map quality that matters .. Eleanor On Sun, 21 Jun 2020 at 15:16, Matthew Snee <

[ccp4bb] Thanks and outcome of ([ccp4bb] Looking for method to find similar oligomeric arrangement)

Dear All Many thanks to Johann for the suggestion of Topsearch - rather pleasingly our tetramer is novel in the tetrameric arrangement, but each of the dimers has its DNA recognition helices in agreement with several hits a win all round Bringing joy to my lockdown. Best Andy

[ccp4bb] Ideas for improving refinement with anisotopic data.

Hi everyone. I have an x ray structure that I am finishing up, and there are a few ambiguous regions where the peptide is poorly resolved. The data is highly anisotrophic, and requires truncation to around 2.4A to achieve acceptable merging stats, although there is data in the "good"

Re: [ccp4bb] AW: [ccp4bb] Looking for method to find similar oligomeric arrangement

WEll I would use PISA first to see if the buried surface areaagrees with my oligamer construction - that uses symmetry.. Then test SSM with the suggested oligamers.. Eleanor On Sun, 21 Jun 2020 at 10:24, Brandstetter Johann < johann.brandstet...@sbg.ac.at> wrote: > Topsearch does that,

[ccp4bb] AW: [ccp4bb] Looking for method to find similar oligomeric arrangement

Topsearch does that, https://topsearch.services.came.sbg.ac.at/ Best, Hans Von: CCP4 bulletin board Im Auftrag von Andrew Lovering Gesendet: Sonntag, 21. Juni 2020 10:51 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Looking for method to find similar oligomeric arrangement Thanks Boaz for

Re: [ccp4bb] Looking for method to find similar oligomeric arrangement

Thanks to all of you pointing me towards ProtCID, but unless I'm mistaken this works only for deposited co-ordinates / PDB entries? I was more looking for something that would take my (yet to be deposited) PDB file, with its inherent tetrametric hth fold, and find similar folds in similar

Re: [ccp4bb] Looking for method to find similar oligomeric arrangement

Hi Andy, Are you familiar with ProtCID? http://dunbrack2.fccc.edu/ProtCiD/Default.aspx Might be relevant. Best, Orly On Sun, Jun 21, 2020 at 12:02 AM Andrew Lovering wrote: > Dear colleagues, > > > I have a structure of a simple, common fold (hth, dna-binding) that I > believe has

Re: [ccp4bb] Looking for method to find similar oligomeric arrangement

Thanks Boaz for the SSM heads up. I was much too DALI-centric! One last point, if anyone can offer an opinion - I presume most methods will match but only within ASU contents. Does any approach utilize deposited "biological unit" classification or (better still) crystallographic symmetry

[ccp4bb] Cold cabinet recommendations for AKTA Pure

Dear All Apologies for being wildly off topic, but we're trying to find a decent cold cabinet for 2x AKTA Pure + F9C + sample pump. Does anyone have any recommendations, especially for sliding door models? Cheers, Alan