Re: [ccp4bb] How to change keyboard shortcuts in Coot

On 15/07/2023 03:22, Gong, Zhen wrote: Dear all, Can anyone kindly tell me how to change the keyboard shortcuts settings in Coot? My “control + g” did not go to the specified atoms anymore. I might have changed the shortcut settings by accident. Thank you very much for your help! Ctrl-G i

Re: [ccp4bb] Ligand superposition!

On 15/07/2023 03:49, Subramanian, Ramaswamy wrote: I have over 50 pdb files that I have downloaded from PDB that all have the same ligand bound. I wamt to superpose the ligands (and move the protein coordinates using that matrix).  The goal is for me to see how difference in ligand environmen

[ccp4bb] short-term postdoctoral position

A short-term (10 months) postdoctoral position is available in my laboratory at the University of Helsinki. You will continue our work on understanding the structure and effect of cancer-causing mutations in RET by combining cryoEM with molecular dynamics (Liu et al. Unexpected structures formed

[ccp4bb] Ligand superposition!

Hi All, I have over 50 pdb files that I have downloaded from PDB that all have the same ligand bound. I wamt to superpose the ligands (and move the protein coordinates using that matrix). The goal is for me to see how difference in ligand environments in different complexes. Is there an easy

[ccp4bb] How to change keyboard shortcuts in Coot

Dear all, Can anyone kindly tell me how to change the keyboard shortcuts settings in Coot? My “control + g” did not go to the specified atoms anymore. I might have changed the shortcut settings by accident. Thank you very much for your help! Best, Zhen #

Re: [ccp4bb] Crystallisation textbook

Dear All, The Acta Cryst F special issue is also a very good resource (although I admit that I am biased). Can be read online here: https://journals.iucr.org/special_issues/2016/crystallization/ or ordered as a book from the IUCr h

Re: [ccp4bb] Crystallisation textbook

You can pre-order the new edition of Crystallography made crystal clear! https://blackwells.co.uk/bookshop/product/Crystallography-Made-Crystal-Clear-by-Arwen-R-Pearson-author-Nicholas-Pearce-author-Jennifer-Wierman-author/9780323910484 I’m definitely going to order a copy - along with Macromolec

Re: [ccp4bb] O-glycans in coot and phenix/refmac

To the point of refining in Phenix, once you have the glycans in place it should be automatic except for the first link of the tree. Send me the model and I can provide the necessary files for refinement. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bi

Re: [ccp4bb] Crystallisation textbook

Dear Mike,I offer you this suggestion :-global.oup.comwhich is in the OUP and IUCr Book Series. Greetings,John Emeritus Professor John R Helliwell DScOn 14 Jul 2023, at 15:19, Hough, Michael (DLSLtd,RAL,LSCI) <69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk> wrote: Hi all,   I'd be grateful f

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Re: [ccp4bb] Crystallisation textbook

When I first started crystallization made crystal clear (by Gale Rhodes) and biomolecular crystallography (by Bernhard Rupp) were my favourites. I think the former may have a new version coming out soon. Best, Omid On Jul 14, 2023, at 08:20, Hough, Michael (DLSLtd,RAL,LSCI) <69715b1ac6c0-d

Re: [ccp4bb] Crystallisation textbook

Of course, having sent this email I found the third edition of the same book from 2021. I would still be grateful for other suggestions though Mike rom: CCP4 bulletin board On Behalf Of Hough, Michael (DLSLtd,RAL,LSCI) Sent: Friday, July 14, 2023 3:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [c

[ccp4bb] Crystallisation textbook

Hi all, I'd be grateful for any recommendations of a good up-to-date textbook covering macromolecular crystallisation. Currently we are using the excellent book by Terese Bergfors (2009) but would be interested if there is anything more recent with discussion around automation, micro-crystallis

Re: [ccp4bb] O-glycans in coot and phenix/refmac

In the monomer library, pyr-SER and pyr-THR links are defined for the O-glycosylation. A monomer should belong to the "pyranose" group in the library (or in a user-provided dictionary). Best regards, Keitaro On Fri, 14 Jul 2023 at 09:22, Jon Agirre <17a7df66b7b3-dmarc-requ...@jiscmail.ac.uk>

Re: [ccp4bb] O-glycans in coot and phenix/refmac

On 14/07/2023 08:52, Jonas Emsley wrote: Dear All We have a crystal structure with O-glycans for the first time attached to a Ser and a Thr sidechain If anyone can recommend the procedure for adding these in coot and refining them in phenix /refmac that would be greatly appreciated Hi J

Re: [ccp4bb] O-glycans in coot and phenix/refmac

To the best of my knowledge, there is no o-glycan equivalent of the Coot glyco plugin. We (as in YSBL, York) are working with others to provide tools to build all kinds of glycans, but there's nothing you can use at this point. I would deal with it like I'd do with other modifications, get monomer,

[ccp4bb] O-glycans in coot and phenix/refmac

Dear All We have a crystal structure with O-glycans for the first time attached to a Ser and a Thr sidechain If anyone can recommend the procedure for adding these in coot and refining them in phenix /refmac that would be greatly appreciated All the best jonas #