Re: [ccp4bb] Tools for identifying possible contaminants

Dear Kyle, Clemens, and all, We use a similar approach at PDB to look for common assemblies, but using the center of mass. The item is not yet public though, but if you send me the values (that can be calculated using gemmi: https://gemmi.readthedocs.io/en/latest/mol.html#model) I can have a

Re: [ccp4bb] Tools for identifying possible contaminants

In fact I believe that is what the SIMBAD script does - searches the PDB archive first for cell dimensions, and only then checks possible MR matches.. On Thu, 4 Jul 2024 at 10:26, Clemens Vonrhein < daef624adb06-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear Kyle, > > I often like lookint at the

Re: [ccp4bb] Tools for identifying possible contaminants

Dear Kyle, I often like lookint at the crystal.idx file [1] for PDB structures with very similar cell dimensions ... and then doing some quick MR to see if one of those sticks out. Easy to fully automate if you have a local copy of the PDB archive, but something like that (bash) cell="30 40 50

Re: [ccp4bb] Tools for identifying possible contaminants

I think this may do the contaminant search you are looking for. ContaMiner (kaust.edu.sa) Best, Mike On Wed, Jul 3, 2024 at 12:04 PM Kyle Gregory < 3632

[ccp4bb] Tools for identifying possible contaminants

Dear all, We have a unit cell that is too small for our expected protein and suspect we have crystalised a contaminant. Does anyone have any recommendations on which tools we could use to identify the possible contaminant? I've tried SIMAD on ccp4cloud and it doesn't suggest anything reasonabl