Re: [ccp4bb] test data sets part II...

I have put some data sets, and data reductions including crystallographic calculations, into XDSwiki: check out http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Quality_Control This is work in progress, so expect additions/changes! And the best is: anyone may contribute ... HTH, Kay

Re: [ccp4bb] test data sets part II...

We put our raw data, plus metadata here: http://www.tardis.edu.au JCSG also make data available, but I think its just an archive, with little or no annotation cheers Ashley On 24/09/2008, at 7:02 AM, afyfe wrote: Dear Tommi, I'm not sure whether 'test data sets part I' relates to the query

Re: [ccp4bb] Troubleshooting protein purification cation IEX

Another option is to purify in denatured condition, then refold. --Chun -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Meg Sent: Tuesday, September 23, 2008 12:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Troubleshooting protein purification cation

Re: [ccp4bb] test data sets part II...

Dear Tommi, I'm not sure whether 'test data sets part I' relates to the query I mailed the other day but, in light of the recent posts regarding fundamental literature, your suggestion seems an excellent one. Perhaps I'm not looking in the right places, but finding examples of image sets

Re: [ccp4bb] recipees for prep of test derivatives

what is it that you want to demonstrate? If it is just for structure solution, would S-SAD phasing be an option? That way all you need is a crystal, probably diffracting to better than, say, 2A. And a little bit of multiplicity. I assume this is feasible for Lysozyme whereas I don't know the

Re: [ccp4bb] Crystallogrphy today

Speaking of good material to attempt to understand crystallographic concepts with , there a video link to the talk given by Airlie McCoy based on the "Liking likelyhood" paper Its on the phaser publications page or at this link htt

Re: [ccp4bb] The mystery of the S-tensor WAS: re-indexing, re-orienting and TLS-tensors

Clemens Sorry my last 2 e-mails probably weren't so clear, because the software may not actually write out S11 & S22 explicitly. Unfortunately there's no consistency on what the programs do write out, so you may need to solve some linear equations for the unknowns S11, S22 & S33 needed to constru

Re: [ccp4bb] The mystery of the S-tensor WAS: re-indexing, re-orienting and TLS-tensors

Hi Clemens The element of S you are referring to is not undefined: the value of one of the diagonal elements of S can be chosen arbitrarily because it makes no difference as far as the individual atomic motions are concerned. The software normally chooses the value for the arbitrary element so tha

[ccp4bb] The mystery of the S-tensor WAS: re-indexing, re-orienting and TLS-tensors

Dear all, a few weeks ago I was wondering how to apply a rotation matrix to TLS-tensors and Ian was so kind to supply us with the corresponding formulas. After looking a bit into it, however, the whole matter seems to be complicated by the fact that one value of S is undefined, however, after

Re: [ccp4bb] Troubleshooting protein purification cation IEX

Another suggestion that comes to mind is crosslinking via Cys, are you purifying under reducing conditions ? Or since you have inclusion bodies they're in general not correctly folded hence expose hydrophobic regions and can interact with other proteins, to avoid unspecific interaction add

Re: [ccp4bb] Crystallogrphy today

Perhaps you could translate and annotate it, then send it to the CCP4BB? JPK ps seriously, why do you say no need for review--is it boring, not well written, obsolete, or what? James is still pretty useful, I think, and that was put out only two years later **

[ccp4bb] test data sets part II...

Also, i think that would be nice if this type of info could be put on the web, part of the wiki for instance.. if there is some consensus to what works + the typical proteins easily available. Tommi Kajander, Ph.D. Structural Biology and Biophysics Institute of Biotechnology University of Hel

[ccp4bb] recipees for prep of test derivatives

Hi, Could anyone give a more or less exact recipee for preparing a derivate for lysozyme or proteinase K? like what used, concentration and soak time. we'd need some data sets for a lab course only thing that really worked so far was lysozyem KI SIRAS (which however doesnt seem to be good en

Re: [ccp4bb] Troubleshooting protein purification cation IEX

Meg, I might add that if you have boiled your samples, you might disregard this: 1) Instead of contamination, you might just be seeing multiple bands due to 'aggregation' of your protein! Make sure you boil the sample prior to loading on gel and also that your loading dye contains SDS,

Re: [ccp4bb] Troubleshooting protein purification cation IEX

Hello Meg, Since your protein is quite acidic, your next step could be e.g. anion exchange - provided that you are able to get the protein into a suitable buffer w/o losing it (since you will pass through the pI). If you can, the simplest way to do so is to add TRIS to the pH4.5 buffer until you g

Re: [ccp4bb] Troubleshooting protein purification cation IEX

Hi, Many things can lead to your observation. Please outline all steps of your purification procedure as it is not clear what is done before and after the Ion Exchange steps. I am not sure if IEF in your emails refers to Isoelectric focusing, as the acronym is usually used?? Couple of s

[ccp4bb] Question: Linux distributions people use

Dear BB, I hesitate to ask this, but here goes. If you are a Linux "admin" user (i.e. the person who installs CCP4) please could you drop me a line (personally, rather than the BB) about which version of Linux you are using. This will allow me to figure out the most popular systems people have,