[ccp4bb] PhD position available at Leicester/ Diamond Light Source

Dear all, We have an exciting PhD project between University of Leicester (Dr Hanna Kwon and Prof Peter Moody) and Diamond Light Source (Dr Pierre Aller and Dr Allen Orville). The project is to study metalloenzymes with time-resolved serial crystallography combined with X-ray emission

[ccp4bb] Refinement of ligand with alternate chemical structure

I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some refinement have noticed partial occupancy of it's hydrolysed form 2x A3, which has a cyclic 2'-3' phosphate on the terminal ribose. I tried fitting both ligands with 50% occupancy, but refinement doesn't allow them to

[ccp4bb] Off topic - 3D models demonstrating drug binding to students

Dear CCP4, I apologize if this is off topic but I thought this may be a good community to ask. Before we re-invent the wheel this end, we are looking for any commercial source of three-dimensional macromolecular models that can be used to teach how drugs are designed to fit to protein targets.

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Hi Stuart, the answer, I think, is here: https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 Pavel On Wed, Feb 15, 2023 at 8:37 AM Stuart McQuarrie < 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote: > I fit a large cyclic ligand cA6 (cylic

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

I thought that REFMAC tolerated dual occupancies if the sum of the two conformers was <= 1.0? Eleanor Will test.. On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie < 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote: > I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some >

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

One may need to set a preference in Coot to allow such a situation to be viewed. Paul helped me but I can't find the email. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email :

Re: [ccp4bb] Off topic - 3D models demonstrating drug binding to students

Hi Ed, The future is already here... and virtual reality is your friend. This is a field that will likely be revolutionized in the near future, and your students would get an advantage by being exposed to these new technologies. You could check the following:

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Dear Stuart, you have to add   allow_duplicate_sequence_numbers() to $HOME/.coot.py in OSX or the appropriate place on Windows. For Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/ directory for configuration - these can be found (added to) the directory in which Coot

Re: [ccp4bb] Off topic - 3D models demonstrating drug binding to students

These magnetically-linking atomically accurate single-atom models look interesting - but I understand they might be too detailed or might shift around inadvertently :Snatoms Online Store - Magnetic Molecular Models for Educationsnatoms.comI also cannot say I used them (but I am always looking for

[ccp4bb] a reminder

Hello All, We have less than one week before the abstract deadline comes to an end for the IUCr 2023 meeting this year in Melbourne. This is a second, and possibly last reminder... For those that would like to present their work at the meeting, it is time to pull everything together.