According to the error message your offending atom has a type:
chemical=FPAF
scatter.lib assigns scattering factors based on chemical type, and there
are ones for "F" and "F-1" but of course not "FPAF" - this would likely
be the source of your problem. The quick fix is to make your own copy
of scatter.lib and edit the files that reference it to pick up the local
copy.
Phil Jeffrey
Princeton
Jian Wu wrote:
> Dear all,
> I am refining a structure in which there is an fluorine atom in the
> inhibtor. When I go on the energy minimization in CNS, an unusual error
> happened to this atom:
>
> Program version= 1.1 File version= 1.1
> CONNECt: selected atoms form 9 covalently disconnected set(s)
>
> list of isolated (non-covalently bonded) atoms:
> --none--
>
> list of isolated (non-covalently bonded) di-atomic molecules:
> --none--
> %XRASSOC-ERR: missing SCATter definition for ( $ RX4 300 FAF )
> chemical=FPAF
> %XRASSOC error encountered: missing SCATter definition for SELEcted atoms.
> (CNS is in mode: SET ABORT=NORMal END)
> *****************************************************
> ABORT mode will terminate program execution.
> *****************************************************
> Program will stop immediately.
>
> I have check the topology file, the paramter file, and the scatter.lib
> file, but found nothing is unusual in these files. Had anyone ever
> encountered this problem before?
> Any suggestion would be welcome and thank you in advance!
> Best Regards,
> Jian Wu
>
> --
> Jian Wu
>
> Ph.D. Student
> Institute of Biochemistry and Cell Biology
> Shanghai Institutes for Biological Sciences
> Chinese Academy of Sciences (CAS)
> Tel: 0086-21-54921117
> Email: [log in to unmask] <mailto:[log in to unmask]>
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