Make sure there is an END statement at the end of your coordinate file.
Axel Brunger
C. Ainsley Davis wrote:
> Hello all,
>
> I have been having major issues with CNS that I havent been able to figure out.
> My protein has 2 molecules in the asu, ds DNA, ions, and a ligand. I have been
> using refmac for refinement but need to make a composite omit map so that I can
> check things out in CNS.
>
> here is the problem
>
> every time I run generate.inp I get errors like this in the logfile
>
> COOR>HETATM 3389 NA NA E 1 -4.719 7.010 17.729 1.00 33.51
> NA
> SEGMNT: 3 residues were inserted into segment " "
> CHAIN> end
> SEGMENT> if ( &ion_rename_$counter = true ) then
> %SEGMENT-ERR: unrecognized command:
> if
> ^^
> %SEGMENT-ERR: unrecognized command:
> if (
> ^
> %SEGMENT-ERR: unrecognized command:
> if ( false
> ^^^^^
> %SEGMENT-ERR: unrecognized command:
> if ( false =
> ^
> %SEGMENT-ERR: unrecognized command:
> if ( false = true
> ^^^^
> %SEGMENT-ERR: unrecognized command:
> if ( false = true )
> ^
> %SEGMENT-ERR: unrecognized command:
> if ( false = true ) then
> ^^^^
> SEGMENT> do (refy=$counter) (attr refx=9999)
> %SEGMENT-ERR: unrecognized command:
> do
> ^^
> %SEGMENT-ERR: unrecognized command:
> do (r
> ^
> %SEGMENT-ERR: unrecognized command:
> do (refy=
> ^^^^
> %SEGMENT-ERR: unrecognized command:
> do (refy=$
> ^
> %SEGMENT-ERR: unrecognized command:
> do (refy=$counter)
> ^^^^^^^^
> %PARSER error encountered: Encountered too many parsing errors.
> (CNS is in mode: SET ABORT=NORMal END)
>
> I have changed all of my files so that CNS will like them. (outputs from coot
> are not liked by cns) I changed the dna using fix_dna_rna indna > outdna. and
> manually changed the c5m for thymine to c5a for cns. Also made sure the sugar
> ring atoms had (') and not (*). I also changed the CD1 ILE to CD ILE because
> CNS hates CD1 ILE for some reason. One of my ligands is funny so I downloaded
> the topology and parameter files from HIcCup and put them in the necessary
> sections in generate.inp. I have run this before when refining a similar data
> set with not as many issues, but I really would like to know what this means.
>
> thanks all
>
> Ainsley
>
> C. Ainsley Davis, Ph.D.
> Post-Doctoral Fellow
> Massachusetts Institute of Technology
> Department of Chemistry 56-546
> 32 Vassar Street
> Cambridge, MA 02142
>
> Phone Number: (617) 258-7021
> Fax Number: (617) 258-7847
>
> E-mail: [log in to unmask]
>
>
--
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web: http://atb.slac.stanford.edu
Email: [log in to unmask]
Phone: +1 650-736-1031
Fax: +1 650-745-1463
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