Re: [ccp4bb] CCP4 release 7.0 update 056

2018-04-27 Thread Doriano Lamba
Dear all, suddenly (i believe after the latest update of Windows 10) when starting ccp4i2 I receive the following message: ** C:\CCP4-7>ccp4i2 CCP4:C:\CCP4-7\7.0 CCP4_SCR:C:\ccp4temp CCP4I_TCLTK: C:\CCP4-7\

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

2018-04-27 Thread IGBMC
Le Vendredi 27 Avril 2018 14:51 CEST, vincent Chaptal a écrit: Just a little remark (I hope I'm not splitting hairs): it is not exact that the alkyl chain "creates a lot of entropy". Instead the mark of dissolution of hydrophobic compounds in aqueous solvent is a strong decrease of entropy du

[ccp4bb] Postdoc and PhD jobs at Oxford

2018-04-27 Thread Elena Seiradake
Dear all, I would like to draw your attention to PhD and postdoc opportunities at Oxford University. We work on the structures and functions of brain receptors. Information on the lab is found here: http://seiradake.web.ox.ac.uk/home Links to the available posts are here: http://seiradake.web.o

Re: [ccp4bb] CCP4 release 7.0 update 056

2018-04-27 Thread Charles Ballard
Dear All (particulary OS X users) A heads up for mac users of DUI, There seems to be a issue (but not every time, and not when we were testing :-) with an illegal access in boost_adaptbx. As the output will testify setting BOOST_ADAPTBX_FPE_DEFAULT=1 allows continuation. Thanks Graeme for s

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

2018-04-27 Thread Wenhe Zhong
Thanks for the thoughtful thought. The alkyl chain has 8 carbons. The scaffold that the alkyl chain attached to has 3 hydrogen bonds donors and 3 H-bond acceptors and with one phenyl ring. The overall cLogP is around 4 — slightly higher than the Lipinski's rule of five. Yes, I have planed to run

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

2018-04-27 Thread vincent Chaptal
Dear Wenhe, A thought came to mind after having read all the other threads, for which I generally agree. An alkyl chain on a molecule (charged? hydrophilic?, you mention a negatively charged binding site) will most likely not lead to micelle formation as the cmc of the object will be most like

[ccp4bb] size exclusion columns

2018-04-27 Thread Mahey, Jas
Dear Hermann Could you please advise where you are based, and I can then get the appropriate Waters specialists to contact you to discuss the options. Best regards Jas Mahey TA Instruments - a Division of Waters Ltd. -Original Message- From: CCP4 bulletin board On Behalf Of Markus He

[ccp4bb] CCP4 release 7.0 update 056

2018-04-27 Thread Charles Ballard
Dear All the latest update is available * monomer library - fixes for ASN, etc * dui (release under osx and linux, alpha under windows) - new interface for DIALS * DIALS - 1.9.2 * XIA2 - 0.5.542 * aimless - 0.7.1 * ccp4i2 - minor interface fixes * ccp4i - minor interface fixes * phaser - m

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

2018-04-27 Thread Frank von Delft
Long alkyl chains tend to bad things to hang onto any compound, if it's to be biologically useful.  Go consult your friendly local medicinal chemist, chances are they'll freak out. Anyway, long alkyl chains LOVE binding to surfaces, which is of course exactly the sort of thing that generates

[ccp4bb] Abstract deadline is TOMORROW for Diffraction Methods in Structural Biology GRS

2018-04-27 Thread Pearce, N.M. (Nick)
Dear BB, Tomorrow is the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be considered for oral

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

2018-04-27 Thread Barone, Matthias
we also do structure-activity relationship and rational drug design. And I agree with Christian: never rely on one single method and try to include a homogenous assay, such as ITC or FT. you mention a tyrosine involved in the binding pocket. Did you try to track the Tyr in FT? best, matthias _

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

2018-04-27 Thread Christian Roth
Anectodal evidence I have heard from colleagues working with things, which are immobilized is that the measured Kd value on the surface can be wildly different from what is measured in solution. A superbinder on a surface might not be as good in solution. There seems still a lot of debate why that