Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hello, Have you tried ISOLDE? Interactive MDFF is really powerful both for fixing models with poor geometry and for improving fit to the map. There is a good tutorial for refinement of a model against a cryoEM map with ISOLDE:

[ccp4bb] Senior Scientist position at Sanofi: Computational Biology , Machine Learning, Protein Design

*Application link: * https://sanofi.wd3.myworkdayjobs.com/SanofiCareers/job/Framingham-MA/Computational-Biology-Scientist--Machine-Learning-in-Large-Molecule-Research_R2561961 * *About the Company: Every day, Sanofi's 100,000 employees are committed to improve the lives

Re: [ccp4bb] real real-space-refinement

Would the stepped refinement protocol in Coot do what you want? It does a real space refinement for every residue automatically. Cheers Christian On Wed, Jul 29, 2020 at 5:20 PM Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear BB, > > > > I would like to do a real

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hi Herman, There is lots of information on CCP-EM's modelling tools here: https://www.ccpem.ac.uk/training/icknield_2019/icknield_2019.php This includes a tutorial on Refmac. As you note this is done in reciprocal space but the CCP-EM pipeline handles conversions from MRC to MTZ format

[ccp4bb] Senior Associate position in Protein Technologies at Amgen British Columbia, Burnaby, BC

Category: Scientific Job ID: R-102000 Location: Burnaby, BC, CA Additional Location: Canada - Mississauga Posted Date: 7/24/2020 Summary Amgen is a global biotechnology company that discovers and develops breakthrough therapies to treat serious human illnesses. Our mission is to serve patients

[ccp4bb] Senior Scientist position at Amgen British Columbia, Burnaby, BC

Category: Scientific Job ID: R-102328 Location: Burnaby, BC, CA Additional Location: Posted Date: 7/29/2020 Title: Senior Scientist – Protein Technologies Team Lead Reports to: Principal Scientist Location: Burnaby *JOB SUMMARY* Amgen is a global biotechnology company that discovers and

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

Dear all, We would like to inform you that the Call for Proposals (regular proposals) is now open for DESY beamline P11 at the PETRA III synchrotron in Hamburg. This call relates to remote and onsite access during the run period January-July 2021. The deadline for submission is

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hi, Try searching ccp-em. Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jul 29, 2020 18:29, "Schreuder, Herman /DE" wrote: Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the other hand, I have not tried to just select the N- and C-terminus for real-space refinement to see what happens. I would prefer to have some script to do it. Best, Herman Von: Eleanor Dodson

Re: [ccp4bb] real real-space-refinement

Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE < herman.schreu...@sanofi.com> wrote: > Dear BB, > > > > I would like to do a real real-space-refinement of a protein against a > cryo-EM map; not the mtz-based Refmac approach. A quick internet search > produced a

[ccp4bb] real real-space-refinement

Dear BB, I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Problems with refinement of nucleic acid structure

Hello, have you tried anisotropic B-factor refinement? It is usually very good at cleaning-up the difference map. At that sort of resolution, you may still have some way to go in the refinement since the R and R-free usually go to about half of what you have, at least with proteins. Best

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Problems with refinement of nucleic acid structure

Sometimes ghost like this mean there is a spacegroup error - absences can be the result of the non-crystallographic translation and not be truly indicitive of the spacegroup. what is the possible spacegroup and what is the NC translation vector? Eleanor On Wed, 29 Jul 2020 at 14:13, Schreuder,

[ccp4bb] postdoctoral position at the Institute for Protein Innovation in Boston, USA

The Bahl Lab at the Institute for Protein Innovation (IPI) in Boston is recruiting Postdoctoral Fellows. We use protein design to accelerate drug discovery and to engineer new lead therapeutic molecules. In addition to traditional academic collaborations, we work

[ccp4bb] AW: [EXTERNAL] [ccp4bb] Problems with refinement of nucleic acid structure

Dear Rafal, At this resolution, one sees many amino-acid side chains with alternative conformation, so it might be a good idea to test if this is also true for nucleotides. Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Rafal Dolot Gesendet: Mittwoch,

[ccp4bb] Improved Carbohydrate Data at the PDB

Dear CCP4BB We have remediated and improved the representation of carbohydrates in the PDB As part of this remediation we have: * Standardized Chemical Component Dictionary nomenclature following IUPAC-IUBMB recommendations * Standardized representation of oligosaccharides *

[ccp4bb] Senior scientist position Protein Purification at Evotec

Dear CCP4 community, We are expanding our Structural Biology group at Evotec and we have many Protein Purification positions open in our Protein Science team. If you are interested, please apply using this link:

[ccp4bb] Error initialising ccpi4i2 in Mac Catalina

Dear all, I don't seem to be able to get a functional installation of ccp4i2 on Mac Catalina. I have downloaded the latest ccp4i2 installer and reinstalled XQuartz, but the application still doesn't open (no errors shown if I open the application on finder) I have then reinstalled in the