Re: [ccp4bb]: refmac5 problem

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Yu Wai Chen wrote:
> 
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> 
> Dear all,
> 
> I am trying to refine my structure with refmac5 but I encountered some
> problems, apparently arose after I have included an acetate ion.  Here
> are the part of the log file that moans:
> 
> #######################################################################
> 
>   NUMBER OF MONOMERS IN THE LIBRARY          :  2407
>                 with complete description    :   336
>   NUMBER OF MODIFICATIONS                    :    37
>   NUMBfmt: read unexpected character
> apparent state: unit -1 named
> last format:
> (6X,I5,A1,A4,A1,A3,A7,3X,3F8.3,2F6.2,10X,A4)
> (10X,A40,A9,3X,A4)
> (10X,A68)
> (10X,A68)
> (10X,I4)
> (7X,I3,1X,A36)
> (7X,A3,10X,I5,5X,A40)
> (12X,A3,4X,A40)
> (6X,3F9.3,3F7.2,1X,A11)
> (5X,A1,4X,3F10.6,5X,F10.5)
> (5X,A1,1X,I3,3F10.6,5X,F10.5,4X,I1)
> (15X,A1,1X,A5,7X,A1,1X,A5,23X,A6,1X,A6)
> (12X,A5,A3,1X,A1,A5,3X,A10,2X,A5,A3,1X,A1,A5,2X,A6,1X,A6,A8)
> (12X,A3,1X,A1,1X,A5,1X,A8,40X,A8)
> (15X,A1,1X,A5,7X,A1,1X,A5)
> (6X,11I5)
> Unit -1 is a (null) formatted internal file
> ER OF LINKS                            :    62
>   I am reading libraries. Please wait.
>       - energy parameters
>       - monomer"s description (links & mod )
> 
>  FORMATTED      OLD     file opened on unit  45
> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
>  Logical name: ATOMSF, Filename:
> /nfs/ind1/people/public/xtal/ccp4-4.1/ccp4/lib/data/atomsf.lib
> <!--SUMMARY_END--></FONT></B>
> 
>  FORMATTED      OLD     file opened on unit   8
> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
>  Logical name: SYMOP, Filename:
> /nfs/ind1/people/public/xtal/ccp4-4.1/ccp4/lib/data/symop.lib
> <!--SUMMARY_END--></FONT></B>
> 
> *** Execution Terminated (115) ***
> 
> #######################################################################
> 
> THese are my lines for the acetate ion:
> 
> ATOM      1  C   ACT T   1      19.045   2.900   0.682  1.00 20.00
> ATOM      2  O   ACT T   1      19.245   3.029  -0.601  1.00 20.00
> ATOM      3  OXT ACT T   1      18.786   3.826   1.525  1.00 20.00
> ATOM      4  CH3 ACT T   1      19.082   1.456   1.153  1.00 20.00
> 
> #######################################################################
> 
> Can someone enlighten me please?
> 


Coordiates OK.
 Problem somewhere in mionomer list I would suspect.
You need to run it in review mode from the GUI to see what sort of
library is generated, then stat again with MAKE CHECK none but including
the new library.

Eleanor