Re: [ccp4bb] clashscore question

Hi Xiaodi, Please read the PDB validation report for the individual clashes and see if these are symmetry or alternate related. If you have been playing around with atomic occupancies, this also affects which atoms are taken into account for the clashscore. Also, which hydrogen model did you us

Re: [ccp4bb] clashscore question

Dear Yu, I think pdb validation server add hydrogen to the structure and then calculate the clashscore. The other methods you mentioned calculate clashscore without adding hydrogen to the structure. Regards Sharan On Tue, Jan 15, 2019, 11:23 PM Xiaodi Yu Hi All: > > I have a pdb file and the c

[ccp4bb] clashscore question

Hi All: I have a pdb file and the clashscores reported from both phenix and MolProbity were around 5, while the clashscore from the pdb validation server is 17. I wonder what may cause the difference? Any suggestion is appreciated. Thank you. Xiaodi ###

Re: [ccp4bb] covalent link to aa

Hi Markus, Did you load the .cif file into Coot before real space refinement? File -> Import CIF dictionary … When you do that, Coot should be able to refine the link and that might then also help for the refinement in Refmac. Bernhard Bernhard C. Lechtenberg, PhD Postdoctoral Associate Riedl L

[ccp4bb] covalent link to aa

Dear all, I have a structure where CYS is bound to OCA (octanoic acid). I started with Jligand and created a CYS-OCA covalent link. It then output a CIF file (verified looks OK). Add the LINK record to PDB file: LINK SG CYS A 161 C1 OCA A 902CYS-OCA Place

[ccp4bb] hybrid photon counter in the home lab

Hi, I would value your opinions in this equipment-related question. Allé et al have compared detector types with a molybdemon source for a small molecule application . Are there similar published comparisons for protein crystallography? What benefit

Re: [ccp4bb] translational NCS & twinning

Dear Eleanor, Many thanks for you comments. I have run aimless/pointless with those data sets having unit cell (134/67, 134/67, 183, 90, 90 120) previously integrated with P31 2 1. Previously, I forced aimless to not determine laue group, to keep the original SG, and now I let aimless determine

[ccp4bb] MRC-IMPaCT PhD -LISCB Leicester & MPL Diamond

*Deadline Sunday 20 January 2019*. The theme for the MRC IMPaCT programme is complex disease. This project studies membrane protein complexes relevant to fibrosis, and funding is for 3.5 years. It will be based within LISCB (Leicester Institute for Structural & Chemical Biology), and is a partner

[ccp4bb] Group Leader position in CryoEM at eBIC - Diamond closing date this wednesday 16th January!

Dear all For all the cryoEM people who clearly avidly follow ccp4 this is a reminder of an exciting opportunity to join eBIC at Diamond as a group leader in CryoEM Full details here: https://vacancies.diamond.ac.uk/vacancy/principal-electron-microscopy-scientist-ebic-368475.html Informal inquir

[ccp4bb] Postdoc position in Structural Biology at the Francis Crick Institute

Dear Colleagues, We are looking for a highly motivated structural biologist to join the group of Katrin Rittinger at the Francis Crick Institute as a postdoctoral fellow. Work in the group is focused on defining the regulatory mechanisms that underlie protein ubiquitination. The successful ap

Re: [ccp4bb] translational NCS & twinning

Donghyuk - testing your "twinning" in a lower symmetry space group can be misleading. Many checks look to see if twin related reflections are similar. But the twin laws are often the same as the symmetry operators, so if you have ignored the true symmetry, you will wrongly assume you have twinning.

[ccp4bb] PostDoc AD

Hello Please find enclosed an ad for a postdoc position in our laboratory. Many thanks in advance. Best regards, Dr. Isabelle M.L. BILLAS, Ph.D. Institute of Genetics and of Molecular and Cellular Biology (IGBMC) Department of Integrated Structural Biology Team 'Large complexes involved in gene ex