I am locked down and dont have access easily to the lsqkab code. Remind me - if/when we are able to go to the University again! to check this.. I am sure you are right - lsqkab certainly predates TER records.. All the best Eleanor
On Tue, 28 Apr 2020 at 14:18, benjamin bax <[email protected]> wrote: > > Hi Eleanor, > Thanks for fix. > > Sometimes I just superpose three atoms (making sure they are not in a > straight line). > But my atom superposition lsqkab script (below) - suggests that lsqkab has > a different atom count than used ‘standardly’. > Has anyone else found this problematic? > > Thanks, Ben > > > cat lsq_compound_new.com > #!/bin/sh > > set -e > # > # nb xyzin1 is reference structure - not moving. > lsqkab xyzin2 ABITIO-p-nh-p-nometal.pdb xyzin1 1S16-on_mola_ndom.pdb \ > XYZOUT abit_nomet_on_1s16.pdb \ > RMSTAB sub_suba_rms.tab <<EOF > # BE CAREFUL - USES OWN INTERNAL ATOM COUNT. > # IN THIS EXAMPLE IT IS ONE OUT. > # I THINK THIS IS BECAUSE TER RECORD IN PDB FILE > # HAS AN ATOM NUMBER RECORD. > # LSQ DOES NOT COUNT THIS AS AN ATOM - SO EVERYTHING > # AFTER THIS IS ONE NUMBER OUT. > #FIT ATOM 2 TO 2 > #MATCH ATOM 2957 TO 2957 > FIT ATOM 5 TO 5 > MATCH ATOM 2953 TO 2953 > FIT ATOM 6 TO 6 > MATCH ATOM 2954 TO 2954 > #FIT ATOM 9 TO 9 > # M#ATCH ATOM 2960 TO 2960 > FIT ATOM 3 TO 3 > MATCH ATOM 2955 TO 2955 > OUTPUT RMS # ! output file RMSTAB with differences > OUTPUT XYZ # ! output file RMSTAB with differences > END > EOF > > > > On 28 Apr 2020, at 11:54, Eleanor Dodson < > [email protected] > <[email protected]>> wrote: > > 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 > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
