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
quick scan though released entries.
Kind regards,
Deborah
On 04/07/2024 10:25, Clemens Vonrhein 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/
--
-------------------------------------------------------------------
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
-------------------------------------------------------------------
########################################################################
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/
