Re: [ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

Dear Paul and Jon, Thank you for your replies and comments. I guess I can provide a bit of background: there are 8 monomers in the asymmetric unit (534 residues each) and each chain is glycosylated with Asn-NAG-NAG-BMA-MAN-MAN (assumed from the electron density map ; the protein was expressed

Re: [ccp4bb] Coot 0.9.5

Thanks a lot, Bill, for your efforts. Best, xavier On 18/3/21 16:18, William G. Scott wrote: With respect to Big Sur, sometimes a picture helps … On Mar 18, 2021, at 8:13 AM, William G. Scott > wrote: I’ve compiled it, but am having trouble with the GUI.  This is

Re: [ccp4bb] Coot 0.9.5

I’ve compiled it, but am having trouble with the GUI. This is not a big sur problem per se, but rather is the newer GTK+3 X-windows-independent interface. When we get it working, it will be a much nicer mac interface. Apple threw OpenGL under the bus in the last couple of OS updates. > On

Re: [ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

Dear Cyril and Paul, COVID struggles permitting, we will _very_ soon have Acedrg dictionaries for most pyranoses in the monomer library. These contain validated conformers, updated torsion restraints and, of course, modern geometry. Cyril: would you like to test these dictionaries with your

[ccp4bb] Postdoc positions in Cambridge

Dear all, A reminder that there are postdoc positions available in our lab in the Department of Biochemistry of the University of Cambridge, UK, to work on structure and function of protein complexes important for DNA replication and repair. The deadline for the application is April 2nd.

[ccp4bb] Coot 0.9.5

Dear all, any hint from where to get precomplied Coot 0.9.5 for Big Sur? Best regards, Xavier -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Re: [ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

The geometry targets for protein are well established (by which I mean "agreed upon") and so the distribution On 18/03/2021 07:19, Cyril Hamiaux wrote: Dear Jasmine (and all), Many thanks for the article. I have a question regarding the Z cutoffs used to flag geometry outliers in the PDB

Re: [ccp4bb] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

Dear Jasmine (and all), Many thanks for the article. I have a question regarding the Z cutoffs used to flag geometry outliers in the PDB validation reports: geometry outliers are flagged with |Z|>2 for ligands (including carbohydrates), but with |Z|>5 for proteins. What is the rational for