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 < 0000daef624adb06-dmarc-requ...@jiscmail.ac.uk> wrote: > 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/ > ######################################################################## 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/
