Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

2021-06-21 Thread Paul Emsley
On 22/06/2021 06:47, Jiang Xu wrote:    I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to

Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

2021-06-21 Thread David Briggs
Hi Jiang Xu, (Phenixbb added as I suspect this is Phenix not coot that has caused your issue) Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input PD

[ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

2021-06-21 Thread Jiang Xu
Hello guys, I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It wor

Re: [ccp4bb] RNA-PROTEIN purification on FPLC

2021-06-21 Thread Artem Evdokimov
Hi 1. Lysate on fplc is messy :) which is why I always do the first step in batch. 2. A good scrubbing with NaOH, trypsin, and a strong chaotropic agent (in series) should take care of the contamination, however it may be easier to find e.g. an old HPLC never used for protein work in order to pur

[ccp4bb] RNA-PROTEIN purification on FPLC

2021-06-21 Thread WENHE ZHONG
Dear members, We are planing to purify RNA only or/and RNA-protein complex on FPLC. The application of the purified materials is for crystallization. However, our concern is that our FPLC has been frequently used in bacterial expressing protein purification including purifying proteins from crude

[ccp4bb] Electron and laser optics postdoctoral/technician positions in New York City

2021-06-21 Thread Anthony Fitzpatrick
The Fitzpatrick lab at Columbia's Zuckerman Institute has multiple openings for postdoctoral research associates and technicians to develop an ultrafast laser phase plate (fitzpatrick-lab.org/pulsed-laser-phase-plate) for cryo-electron tomography funded by the Chan Zuckerberg Initiative *(*Frontier

Re: [ccp4bb] Enzyme Vmax and Km

2021-06-21 Thread Prem Prakash
Dear Tristan and all my ccp4bb members, Thank you so much for your valuable suggestions into the enzyme kinetics issue I have been facing. It gave me new insights to design my experiment and I started working on those inputs. Thank you all once again. It's very helpful. With kind regards Prem O

[ccp4bb] Call open for BAG beamtime at DESY beamline P11, PETRA III

2021-06-21 Thread Hakanpää , Johanna
Dear all, Please note the approaching deadline for submission of Block Allocation Group (BAG) proposals for DESY beamline P11 at the PETRA III synchrotron in Hamburg. Proposals are to be submitted via https://door.desy.de The deadline for submission is ---