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
<0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> 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 <car...@med.unc.edu
<mailto:car...@med.unc.edu>> 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 <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
>
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