Re: [ccp4bb] COOT 1.1 and DNA mutation

On 25/04/2024 16:07, Simon Vecchioni wrote: -- Paul, Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works like a charm! I would ask about two other DNA features-- 1) The [add terminal residue] button seems unresponsive for DNA, I see what you mean. From the

[ccp4bb] NYSBC-SEMC 3D ED/MicroED short course - Nov 4-6, 2024 (NYC, USA)

Dear all, We will offer our 2nd 3D ED/microED short course November 4-6, 2024 in NYC. The agenda includes in-depth lectures on theory; and hands-on practicals covering sample preparation, setting up a TEM for data collection and data processing. For those ready for further practice (or a

[ccp4bb] Postdoctoral Research Associate – Biochemistry/Biophysics

The Diffraction Group in the Neutron Scattering Division (NSD) at Oak Ridge National Laboratory (ORNL) has an immediate opening for a postdoctoral Biochemist or Biophysicist to join a multi-disciplinary research team in development and application of paramagnetic labeling and proton

Re: [ccp4bb] COOT 1.1 and DNA mutation

Paul, Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works like a charm! I would ask about two other DNA features-- 1) The [add terminal residue] button seems unresponsive for DNA, and is often quite useful; 2) There was a button chain in v0.8.9 to add base pair

Re: [ccp4bb] add ligand with AceDRG

The PDB has reserved the following codes for unknown ligands: DRG INH 01 - 99 Using one of these should not cause you the described problems. I successfully used 99 just last week. If you try to use 999 or LIG these will not work, there are ligands assigned to those codes. Diana Sent

[ccp4bb] EMBO practical course: Structure, dynamics and function of biological macromolecules by NMR

Dear colleagues, Applications are open for the EMBO practical course: “Structure, dynamics and function of biological macromolecules by NMR”. The application deadline is the 1st of May 2024. The course will be held from Friday the 30th of August until Friday the 6th of September 2024 at the

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, If you could run from command-lines, it will be easy to solve this problem. try from command-line, type acedrg -i "your_smiles_string" -r your_3_letter_code -o your_out_file_name For example, acedrg -i "C[C@@H](C(=O)O)N" -r UNL -o UNL You will get a file called UNL.cif, which

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, Why can you only use "taken" three letter codes? In the "output monomer" box, you should be able to enter whatever you'd like for the "Three letter code for output monomer". In the attached image, this is shown as "DRG" but can be changed to any 3 letter code of your choice.

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, Can you manually edit the restraints file using TextEdit and find and replace and the pdb file of course? Other option is to use Grade or Grade2 and the smiles string if you have this software installed. I often find this easier than ccp4i2. Best regards and good luck! Maria >

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, In CCP4Cloud, the equivalent task will generate the files using a 'free', unused code, if nothing is entered in the relevant box. However, not sure if CCP4I2's task will do the same, but worth trying. Hope this helps, Andy From: CCP4 bulletin

[ccp4bb] add ligand with AceDRG

Hi all, I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with existing library entries. Is there any way

Re: [ccp4bb] Microscope camera

Have you considered a Raspberry Pi with camera, or camera mount with your existing lens: https://www.raspberrypi.com/products/#cameras-and-displays Photos and livestream will be easy to set up. You could try motioneye to give you a livestream and take pictures on demand, or at defined time

Re: [ccp4bb] Microscope camera

Dear Pat, we are facing the same problem and the most effective solution I found is to print support for smartphones, which today offer incredibly good cameras. Here are two examples of open access designs: https://www.openocular.com/

Re: [ccp4bb] Microscope camera

Hi Pat Depends on how much you want to spend. I’d start with a web search for “webcam astrophotography”, which should show options on how to remove a webcam’s lens and mount the cam (not the kens, of course!) on another optical instrument. Back in the day, I had a Philips webcam that had a

[ccp4bb] Postdoc position Structural Virology, BNITM & CSSB Hamburg

Moin! I have a 2-year postdoc position to fill in the field of structural biology of protein-RNA complexes. Location is beautiful Hamburg, Germany, with top-notch research facilities, great collaborators and a fun and motivated team. Application deadline is May 19th. More details here: