[ccp4bb] COMPPA symposium registration deadline May 1!

Hi all, The deadline to register for the COMPPÅ symposium at Columbia University in New York (covering production, structure determination, functional analysis and engineering of membrane proteins, 17-19 June 2018) is coming up in less than a week - May 1! Register here to attend and/or

Re: [ccp4bb] Compound with flexible conformation but nM Kd

Hi Philippe, The affinity was measured by SPR where we immobilized the protein on the chip. One thing I forgot to mention is that the association rate (kon) shown in SPR experiment for this compound is faster (>10-fold faster) compared to other analogues with similar koff. There is a pi-pi

Re: [ccp4bb] What's happened over the last five years with high-throughput protein crystallization screening?

Unfortunately it is unlikely that the costs for robotic equipment (at least the larger scale equipment) will come down much. It is effectively all ‘bespoke’ equipment and will never benefit from high volume manufacturing (nothing like phones or cars). How many crystallisation centres are needed

Re: [ccp4bb] What's happened over the last five years with high-throughput protein crystallization screening?

Dear Daniel, I appreciate you for your really worthwhile comments that would be useful for other scientists in this field. Thanks. Frank On Thu, Apr 26, 2018, 17:13 Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: > I skimmed your paper, and overall it looks like a good overview >

Re: [ccp4bb] What's happened over the last five years with high-throughput protein crystallization screening?

I skimmed your paper, and overall it looks like a good overview of high-throughput protein crystallization. However, I was surprised that no mention was made of Formulatrix Rock Maker software, which is an excellent computer-aided graphical tool for designing crystallization screens rapidly.

Re: [ccp4bb] Compound with flexible conformation but nM Kd

For proteins in membranes, or proteins purified in the presence of detergents and/or lipids, the active site is sometimes surrounded by a hydrophobic mileau. The actual concentration that the binding site sees is then dependent on partitioning of the ligand between the water (where its

Re: [ccp4bb] Compound with flexible conformation but nM Kd

Le Jeudi 26 Avril 2018 16:50 CEST, WENHE ZHONG a écrit: Just to be sure: how was the nM affinity evaluated ? By in vitro measurements, or by obtaining an IC50 by tests on cells ? Of course, if you are mentioning an IC50, you may have a measurement of the

[ccp4bb] 11th CCP4/APS Crystallographic School in the US

Just a friendly reminder that the deadline for applying the upcoming CCP4 school at APS is next Wednesday (5/2/2018), please apply or finish your application (if you have already applied) if you wish to participate in the school. Please let us know if you have any questions/concerns.

Re: [ccp4bb] size exclusion columns

Hi Markus, just be aware that silica-based SEC columns are very sensitive to alkaline pH conditions, so you should not use them at pH higher that 7.5 We found that to be a limitation and thus chose polymer-based columns. Hth, ciao, Sebastiano > On 26 Apr 2018, at 18:03, Markus Heckmann

[ccp4bb] size exclusion columns

Dear all, We are looking for a size exclusion chromatography column (silica-based) for protein purification prior to a MALS-detector. We looked for (www.waters.com BEH-450), Sepax (Unix-C 300) and Phenomex (BioZen SEC-3). Any 'column' tips or recommendations when dealing with large proteins

[ccp4bb] Compound with flexible conformation but nM Kd

Dear Community, A little bit out of topic here. We are applying the structure-based approach to design compounds that can bind our protein target. We have synthesized a series of analogues based on the same scaffold with different substituents at one particular site. The most potent analogue

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Just to make the point that you are not alone, I have observed the same issue on Mac with CCP4-installed Coot 0.8.9.1 using latest OS and Xquartz. This started happening with a recent update. Interestingly, the 'Edit Chi Angles' dialogue now allows us to modify non-chi angles as well (not

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Update 055 should have reverted out ASP, and update 056 (coming real soon now) should fix the other issues. Charles -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of "Weiergräber, Oliver H." Sent: 26 April 2018 15:06 To: ccp4bb

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Indeed, update 54 from Mar 29 seems to have messed up several monomer definitions and/or their handling in coot (the version distributed with ccp4): - GLU and ASP contain lines referencing GLN and ASN, respectively, preventing coot from finding any chi angles. - For GLN, chi angles appear twice

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Oops - oh dear - GLN labels should* NOT *appear in a list devoted to GLU!! Well spotted.. Eleanor On 26 April 2018 at 10:34, Chris Richardson wrote: > Many thanks for explaining where it is going awry. > > Looking at GLU.cif in the monomer library that is part of

[ccp4bb] Postdoctoral position, Cambridge

A postdoctoral position is available to work on a Wellcome Trust funded project to investigate the molecular mechanisms of regulation of alternative pre-mRNA splicing in the group of Prof. Chris Smith (https://www.bioc.cam.ac.uk/research/uto/smithc

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Many thanks for explaining where it is going awry. Looking at GLU.cif in the monomer library that is part of the CCP4 distribution, it contains the following lines: GLN chi1 N CA CB CG 180.000 15.000 3 GLN chi2 CA CB CG CD 180.000

[ccp4bb] MicroMAX research engineer opening at MAX IV

Dear all, A permanent position as Research Engineer for the recently funded microfocus and serial crystallography beamline MicroMAX is now available at the MAX IV Laboratory. For more information and to apply please follow this link: https://lu.varbi.com/en/what:job/jobID:203507 or see the

[ccp4bb] 2 Postdoc positions at Fondazione Ri.MED - Palermo

2 PostDoctoral positions are available in the Structural Biology and Biophysics Unit @ Fondazione Ri.MED (www.fondazionerimed.eu). The successful candidates will carry out scientific projects in the field of structural biology and biophysics aimed at understanding the molecular mechanisms

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson wrote: > > I've just compiled Coot on the same Mac using Fink, and the dialogue for this > version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the > same residue. From a quick look at the Fink

[ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

?We have an issue with the 'Edit Chi Angles' dialogue in Coot on Macs using the version of Coot bundled with CCP4. For some residues - such as Glu - the dialogue only shows the C <--> CA angle. If you tick the 'Add Chi Angles for Hydrogens' box, it adds CA <--> N. I've just compiled Coot on

Re: [ccp4bb] According correct space group assignment...

Is this another example of crystallising the reagent and not the desired material? No wonder molecular replacement failed with a DNA search model . Eleanor On 25 April 2018 at 20:06, George Sheldrick wrote: > Dear Rafal et al, > > With some help from Kay I think that