In my experience, lsqkab wouldn’t orient nucleic acid atoms, and I think Eleanor once told me I needed a different alternative for nucleic acids. If this is no longer true, I’m happy to learn of it.
Charlie On Apr 28, 2020, at 6:40 AM, benjamin bax <ben.d.v....@gmail.com<mailto:ben.d.v....@gmail.com>> wrote: HI Fred, I still use command line version of lsqkab to do this kind of DNA fitting - script below only uses mainchain atoms (not bases) which helps if you have different DNAs. Chain E and F are DNA. Ben ./lsq-hinge-6fqv-bin-EV-B.com<http://lsq-hinge-6fqv-bin-ev-b.com/> > lsq-hinge-6fqv-bin-EV-B.log cat lsq-hinge-6fqv-bin-EV-B.com<http://lsq-hinge-6fqv-bin-ev-b.com/> #!/bin/sh set -e # Obtain NCS rotation/translation relating CHAIN R to CHAIN S # # nb xyzin1 is reference structure - not moving. lsqkab xyzin2 ./6fqv-binary-B-on-2XCS-ToprimB.pdb xyzin1 ./2xcs-c1a.pdb \ XYZOUT binaryB-on-3-6E-15-18F.pdb \ RMSTAB test1.tab <<EOF # # DNA fit two strands - trying for just backbone. # FIT RESIDUE MAIN 3 TO 6 CHAIN E MATCH RESIDUE MAIN 3 TO 6 CHAIN E FIT RESIDUE MAIN 15 TO 18 CHAIN F MATCH RESIDUE MAIN 15 TO 18 CHAIN F OUTPUT RMS # ! output file RMSTAB with differences OUTPUT XYZ # ! output file RMSTAB with differences END EOF On 24 Apr 2020, at 12:08, Fred. Vellieux <frederic.velli...@lf1.cuni.cz<mailto:frederic.velli...@lf1.cuni.cz>> wrote: Hi folks, Some of you may have had to do this already. Either in the lab or more recently perhaps from home. I have two structures that I wish to superpose (two protein:dsDNA complexes). Not using the protein part, but superposition through the dsDNA. I'm not quite certain what is the "best" way of doing this. Your suggestions will be appreciated, thanks. Fred. Vellieux -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
