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 90 90 90" # your cell maxd=2 # max deviation (A and degree) [ ! -f crystal.idx ] && wget -q https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx awk -v cell="$cell" -v maxd=$maxd 'BEGIN{ i=split(cell,c) } /CRYST1/{ for(i=1;i<=6;i++) { d=c[i]-$(i+2);if(d<0)d=-d if(d>maxd)next } print }' crystal.idx would give you a first listing ... Cheers Clemens [1] https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx On Wed, Jul 03, 2024 at 03:54:20PM +0000, Kyle Gregory wrote: > 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 reasonable. > > Kind regards, > Kyle > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
