I MEANT to upgrade lsqkab to accept DNA, and there is a small possibility that I did! Cheers Eleanor
On Tue, 28 Apr 2020 at 11:52, Carter, Charlie <[email protected]> wrote: > 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 <[email protected] > <[email protected]>> 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 <[email protected] > <[email protected]>> 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
