I noticed the same problem with more recent versions of CCP4 (up to and including 6.5.001) but failed to report it….
It seems that the problem occurs regardless of the atoms chosen for selection - main, side or all - and with both v2 and v3 PDB files.
The 'LSQ Superpose’ in Coot can superpose nucleic acids, but it is seemingly not possible to define non-contiguous selections.
Rob
> On 04 Feb 2015, at 17:30, Carter, Charlie <[log in to unmask]> wrote:
>
> I'm (still) using ccp4.6.1.1.
>
> Scripts that used to superimpose one tRNA on another now all return the error
>
> YOU HAVE FAILED TO FIND ANY ATOMS TO FIT
>
> I've looked high and low for a reason for this and failed. The pdb files themselves look normal and behave well in PYMOL. They have CRYST1 cards. I cannot even superimpose a file on itself!
>
> Anyone have any suggestions?
>
> Thanks so much,
>
> Charlie
>
> here is what I'm trying to implement:
>
> lsqkab XYZIN1 $1 XYZIN2 $2 XYZOUT $2_$1 >$2_$1.log << END-lsqkab
> FIT RESIDUE MAIN 2 TO 6
> MATCH 2 to 6
> FIT RESIDUE MAIN 68 TO 72
> MATCH 68 to 72
> OUTPUT XYZ
> END
> END-lsqkab
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