Re: [ccp4bb] small molecule library

2009-10-28 Thread Flip Hoedemaeker
A company called ZoBio screens their 2,000 fragment library with NMR, cool technology. Don't know about € www.zobio.com Flip Sridhar Prasad wrote: Zenobia is a good place to look for, they can even customize it your needs. www.*zenobiatherapeutics*.com Sridhar Date: Wed, 28 Oct

Re: [ccp4bb] Parallelization of Phaser and other programs part of CCP4

2009-10-28 Thread Randy J. Read
There's OpenMP parallelization of some of the most CPU-intensive parts of molecular replacement in Phaser, in the versions released recently in Phenix and hopefully in the next CCP4 release. However, OpenMP is not turned on by default in the compilation of the binaries released with Phenix, so

[ccp4bb] Post-doctoral position, IFOM-IEO-CAMPUS, Milan

2009-10-28 Thread Sebastiano Pasqualato
Posted on behalf of Prof. Francesco Blasi, who might be directly contacted if interested (check http://www.ifom-ieo-campus.it/research/blasi.php for contacts) Post doctoral position available from January 2010. Laboratory: Prof. Francesco Blasi, IFOM (Foundation FIRC Institute of

Re: [ccp4bb] Inclusion bodies centrifugation

2009-10-28 Thread Ezra Peisach
Artem has already responded - but I believe you will pull down the cellular debris with the IB. In my prior experience, post centrifugation, you can wash the IB/debris with increasing amounts of urea in you solubilization - and you may find that the other cellular debris stays in solution

Re: [ccp4bb] SAD phasing at home source

2009-10-28 Thread Flip Hoedemaeker
Yep, solved a structure at Cu K-alpha once with the sulfur signal, resolution 1.7A and a redundancy of 50 or so did the trick. Actually, one of the sulphurs we found was an ordered SO4 molecule, so if you have that in your crystallisation condition it might be a bonus... Flip Watanabe

Re: [ccp4bb] Inclusion bodies centrifugation

2009-10-28 Thread R.M. Garavito
As Artem and Ezra have already mentioned the basic aspects of isolating IBs, I should point out that most people wash the pellet of the first low-speed centrifugation 2-3 more times. While Ezra suggests using increasing amounts of urea, you may have to tailor the composition of the wash

Re: [ccp4bb] Minimum hardware requirement of Mac OSX for CCP4

2009-10-28 Thread William G. Scott
On Tue, Oct 27, 2009 at 02:13:48PM +0100, Dirk Kostrewa wrote: I agree with Ronnie Berntsson and Roger Rowlett. The only thing that you can't do on those machines is to work with Coot in stereo 3D. Currently, you would need a MacPro and a special Nvidia Quadro graphics card (and stereo

[ccp4bb] San Diego Crystallography Short Course Dec 14-15, 2009

2009-10-28 Thread Bernhard Rupp
Dear All, for those who need an excuse to escape the winter chill - I have scheduled a short-course on Biomolecular Crystallography/SBDD in San Diego/La Jolla. Fee includes a copy of my book. Details: http://www.ruppweb.org/workshops/Molsoft_2009.htm Best wishes, BR

Re: [ccp4bb] off topic, design of a self-cleaving tag

2009-10-28 Thread Pascal Egea
Hi Daniel, look at this the Profinity eXact Fusion-tag system from BioRad* * the protease i fused to your protein and self activated by halides (F or I I think). Cleavage in on column. The principles is clever, now the cleavage conditions may not suit to your protein, but it seems to work. This

Re: [ccp4bb] off topic, design of a self-cleaving tag

2009-10-28 Thread artem
Good times :) When you patent this design, be sure to give royalties to all the contributors. Daddy needs a new Ferrari. I assume you've seen Inteins already, right? Cleavage induced by DTT or BME. Artem Hi, We would like to design a self-cleaving tag. It will be similar to the one Roger

Re: [ccp4bb] trouble running coot on MacOSX 10.5

2009-10-28 Thread Pierre Aller
Hi Rui, to get it work, I would make sure that I have the last version of X-code tools, and update X-quartz with the last version 2.4.0, you can download it here: http://xquartz.macosforge.org/trac/wiki I would also update fink and the source list which are different for Intel and PPC: check

[ccp4bb] offtopic: screening compounds libraries for binding via crystallography

2009-10-28 Thread Francis E Reyes
Hi All I'm interested in screening small molecule libraries against my xtal for potential binders. There are many papers that cover this (http://www.nature.com/nbt/journal/v18/n10/abs/nbt1000_1105.html , for example). If you have had experience in this field, please email me privately as

[ccp4bb] data reduction

2009-10-28 Thread Alexandra Deaconescu
Dear all: I am trying to solve a structure from apparently a hexagonal crystal. I indexed and scaled data in P6 in Scalepack (with merging) then used Scalepack2mtz (with ensure unique reflections and add Rfree as well as the truncate procedure), and then attempted to run molecular