[ccp4bb] PhD position in the Leicester Institute of Structural and Chemical Biology

Dear colleagues, My lab is hiring a highly motivated PhD student interested in biochemistry and structural biology of DNA replication proteins. The lab is located in the Leicester Institute of Structural and Chemical Biology (LISCB), which hosts a new Cryo-EM facility featuring a 300keV Titan

[ccp4bb] CCP-EM Spring Symposium IV: 11-12th April 2018 - Registration now closes Wed 7th March

Dear all, Due to the recent bad weather we have extended the registration period for the Spring Symposium: it will now close this Wednesday (7th March). Please do register by then if you would to attend: http://www.cvent.com/d/9tq4ln This conference aims to provide a forum to highlight state of

[ccp4bb] Small molecule not refined in coot.

Dear all, I am actually dealing with a structure containing an unnatural ligand. I generated the pdb file by drawing it on PRODRG server, I did a manual pre-fit in the map using coot and I manually merged the pdf file of my protein with the one of the ligand. After that I did few cycles of refinem

Re: [ccp4bb] Small molecule not refined in coot.

Hi Michel, If your ligand is designated as DRG in your pdb then refinement programs will anticipate that it is: Chemical Description Name5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE Formula C12 H11 N3 Formal charge 0 Molecular weight197.236 g/mol Component type NON-POLYMER If this is

[ccp4bb] Interfaces

Good morning all, I need to identify my dimer and tetramer interfaces, and point them out in Pymol. Any website/program/script suggestions? I tried PISA, but it only shows me some residues from some interfaces, I need something more "complete". Thank you very much, Lorenzo

Re: [ccp4bb] Interfaces

Can you define "more complete"? What information do you require that PISA does not provide? This way you may get specific recommendations/suggestions. Eugene On 5 March 2018 at 14:02, Lorenzo Briganti wrote: > Good morning all, > > > I need to identify my dimer and tetramer interfaces, and po

[ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

Hi Colin and Michel, In my experience, both refmac and coot will use the most recently read-in cif dictionary and there is no need to try to find an unique identifier for each new ligand one uses. The new dictionary overrides the old one. Finding a unique identifier for each new ligand would be

[ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

PS: If you have two different home-brewn ligands, you have to rename one of them (pdb and cif), otherwise the same dictionary will be applied to two different ligands. Also make sure your cif file is a dictionary and not just a coordinate file. HS Von: Schreuder, Herman /DE Gesendet: Montag, 5.

[ccp4bb] help

Hello all Does anyone knows of a review that highlights the first examples of the use of NMR combined with X-ray crystallography to solve the structures of proteins thanks chandra

[ccp4bb] Residential School on Medicinal Chemistry and Biology in Drug Discovery (ResMed): A Comprehensive One-Week Course

All, I was asked by the meeting organizers to let the CCP4 community know about the 2018 Residential School on Medicinal Chemistry and Biology in Drug Discovery.See below for information about the course and contact information. Sincerely, Corey - Dear all, Th

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

Herman is right - as long as refmac reads your generated DRG that is the dictionary it will use.. My way of doing this sort of thing: Start with COOT with the DRG coordinates and ProDRG dictionary and try a bit of real space refinement. Coot should move the coodinates a bit and you should see som

Re: [ccp4bb] help

Llok at this paper: Does NMR Mean “Not for Molecular Replacement”? Using NMR-Based Search Models to Solve Protein Crystal Structures The references there clainm to give the first instance of success... And Hi Eleanor On 5 March 2018 at 13:51, Chandra wrote: > Hello all > > Does anyone know

[ccp4bb] Postdoctoral Position in Structural Biology

Postdoctoral Position in Biochemistry and X-ray Crystallography At Rice University A postdoctoral position in structural biology is available in the Shamoo Lab at Rice University. The successful candidate must have experience in X-ray crystallography as well as biochemistry. Candidates should ho

Re: [ccp4bb] A helix with leucine repeats

Could it be a member of a coiled coil at some point in its lifetime, as a part of its function in regulating position or activity of this receptor? Does the helix have sequence similarity to other coiled coils? see https://www.uniprot.org/help/coiled for a primer on the topic. Looks fun! Emily.

[ccp4bb] Postdoctoral Position

POSTDOCTORAL FELLOW POSITION AVAILABLE at the Laboratory of Protein Structure of INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY in Warsaw, Poland. Laboratory of Protein Structure seeks a researcher with a PhD degree to study the mechanisms of DNA repair. Laboratory Interest Laboratory of

[ccp4bb] PhD student position available

PhD STUDENT POSITION AVAILABLE at the Laboratory of Protein Structure of INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY in Warsaw, Poland. Laboratory of Protein Structure seeks PhD student to study the mechanisms of DNA repair. PhD fellowship is funded in frame of National Science Cent

Re: [ccp4bb] does 12 A diffraction worth optimization

In addition to the other useful advice offered, I’d also suggest determining if the whole complex or just the DNA fits in the asymmetric unit. Particularly if the crystals are hexagonal rods or plates, you might have DNA-only crystals. ~~~ Phoebe A. Rice Dept. of Bio

[ccp4bb] 2x Postdoctoral Positions in Structural Biology

Hi All, We are seeking two junior postdoctoral researchers with demonstrated expertise in biochemistry and structural biology and an interest in the structure and function of ligand:receptor and antibody:receptor complexes in immunity. The appointment will be based at the Monash University Biomedi

[ccp4bb] Off-topic question

Dear All, We are trying to identify/sequence a DNA/RNA fragment (around 100bp) which was co-purified along with our protein. The expression was done in E.coli. Any suggestions on how to do this. Thank you. Jobi

Re: [ccp4bb] Off-topic question

Hi Jobi, Phenol/CHCl3 extraction, iPrOH precipitation and then nucleic acid sequencing. Best regards,Philippe Philippe BENAS, Ph.D. Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS Faculté de Pharmacie, Université Paris Descartes Case 48 Av, de l'Observatoire F-75270 PARIS cedex

Re: [ccp4bb] Off-topic question

Hi, I was going to suggest the same but since it has already been said, here’s a cheeky suggestion: you could try determining the crystal structure of the complex and get a direct sequence readout for the nuclei acid. Best, Debanu > On Mar 5, 2018, at 9:34 PM, Philippe BENAS > <0d88e888355