Re: [ccp4bb] Symmetry Operations

you can fit your model chin A over chain B First save chain A only to a new model either in COOT or outside by editing so now you have two Models - one A B C etc , and one only A Calulat SSM. overlap or some such instruction of A over B and change CHAIN ID to X say Now repeat with SSM overlap A t

Re: [ccp4bb] Sugar-Pi-stacking

Hi Bernhard, the interaction you are referring to is usually referred to as CH-pi interaction and not 'stacking', and that notation implies, as was pointed out, that the hydrophobic face of pyranose rings (most often GAL) is positioned such that the CH bond vectors interact with the aroma

Re: [ccp4bb] Sugar-Pi-stacking

Thanks to all the respondents. Very useful links on a generally interesting topic. I was pretty sure that this is another case of imprecise notation/definition because even with my limited QM I cannot see a true pi-stacking in the sense of the narrow definition. But, it seems to be frequent

Re: [ccp4bb] A question about Cys and fluoro benzene ring

Dear Cheng, it is possible that the sulfhydryl of the cysteine might have reacted with the methyl fluoro benzyl group via nucleophilic aromatic substitution. Fluorine is not the best leaving group among the halides but it would certainly allow this especially if the ligand-protein incubation ti

[ccp4bb] Symmetry Operations

Dear Phenixbb and CCP4bb members, I'm currently refining a structure and facing some problems. It's originally a tetramer in solution, but I could only solve it in P1 group, with 8 molecules in the asymmetric unit (two tetramers). One of my chains is complete, but the others present some signi

Re: [ccp4bb] Sugar-Pi-stacking

Hi Bernhard, The aromatic-carbohydrate (the hydrophobic face of carbohydrate) was first reviewed in Weis and Drickamer 1996 review in Ann. Rev. Biochem. 65, 441-473 (see their Fig. 5). They didn't use the term Pi interaction though for the reason Ian mentioned I suppose. Regards,          

Re: [ccp4bb] Sugar-Pi-stacking

Dear Bernhard, the explanation can be found in here with additional references in. J Am Chem Soc. 2015 Dec 9;137(48):15152-60. doi: 10.1021/jacs.5b08424. Epub 2015 Nov 30. Carbohydrate-Aromatic Interactions in Proteins. Hope tha

Re: [ccp4bb] Sugar-Pi-stacking

Hi Bernhard Greetings! I don't see how an aromatic-aliphatic interaction can be classed as pi-stacking. Surely it's just a normal dispersion interaction ( https://en.wikipedia.org/wiki/London_dispersion_force)? Cheers -- Ian On 23 August 2017 at 18:18, Bernhard Rupp wrote: > Hi Fellows, >

[ccp4bb] Sugar-Pi-stacking

Hi Fellows, there are some smart chemists amongst you, so I wonder - what precisely am I to understand is the nature of pi-stacking between an aromatic residue or (whatever pi-orbital moiety) and a sugar moiety, disaccharide etc.? Thanks for your help, BR -

[ccp4bb] Research Technician (Structural biology) position at SGC, University of Oxford

Dear all, We are advertising a research technician position in the Metabolism and Organelle Biogenesis group at SGC University of Oxford, which processes a variety of human medically-relevant proteins in recombinant expression systems, and purifies the proteins for structural and biophysical studi

[ccp4bb] Can not use system browser open external links (macOS Sierra)

Dear all, I hope to open a external links by double click the link in qtRView 1.16(ccp4 log viewer), but no response, and I check the preference, it seems ok. My OS is "macOS Sierra,Version 10.12.6" and the CCP4 version is 7.0.0.36. But that link can be open easily in Linux system with the sa