[ccp4bb] Funded PhD position near Paris, France: AI-powered prediction of protein-nucleic acid interactions

Dear all, please find below an announcement for a funded PhD position on the development of deep learning approaches to predict interactions between proteins and nucleic acids. The deadline for application is 30 April 2023. Best regards, Jessica Andreani Scientific project Interactions between

[ccp4bb] refmac output query

Dear All, A quick question about Refmac on ccp4i. When refining an RNA oligonucleotide structure using the findwaters option, the pdb output labels all the atoms as HETATM (inluding the original RNA atoms which were not so labelled in the input pdb). It is of course trivial to correct this, but

Re: [ccp4bb] Covalent link with AceDRG

Dear Marian, How do you know that it’s still a double bond? Is it due to the way that it’s displayed in Coot, or based on the interatomic distances after refinement? Could you have a look in the AceDRG link dictionary (.cif) and confirm the order of the bond? Search for a “_chem_mod_bond” loop

[ccp4bb] Covalent link with AceDRG

Dear all, I'm having an issue running AceDRG for making a covalent link between a compound (with a double bond) and a target His (linking atom NE2). I am running the program in ccp4i2 (ccp4-7.1.018). I have, of course, include the .cif file of the compound (obtained from SMILE using eLBOW) and

[ccp4bb] Postdoctoral Fellow for Synchrotron MX Data Acquisition and Analysis

Dear Colleagues from the CCP4bb, Paul Scherer Institute in Switzerland is hiring a postdoctoral fellow for a project to develop a NextGen Detector Control Unit. The project is realized together with DECTRIS, leading manufacturer of hybrid pixel X-ray detectors, and supported by Innosuisse (Swis

[ccp4bb] Call for beamtime proposals at Diamond Light Source. Deadline 1700 29th March 2023

Dear All The call for proposals via peer-review for non-proprietary access to Diamond MX beamlines from October 2023 until March 2024 is now open (https://www.diamond.ac.uk/Users/Apply-for-Beamtime.html). The deadline for this call is Wednesday 29th March at 17:00 hrs UTC+1/GMT+1. Diamond Ligh

Re: [ccp4bb] anomalous data usage

I believe there are many advantages to storing things *internally* as data objects with metadata instead of as columns of an MTZ file. How many students know what FP,SIGFP mean? And how many know that the FP,SIGFP columns in Refmac's HKLIN are not the same as the FP,SIGFP columns in HKLOUT? In an i

Re: [ccp4bb] anomalous data usage

We are hitting the same problems also with students (so no rigidified brains I think) ... the concept of "files" seems absolutely natural (also to them) and when they ask about solving more tricky problems in i2 ... we do the obvious, go back to ccp4i. I2 is fine when things are smooth and easy.