Re: [ccp4bb]: watertidy

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

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> Jan Dohnalek wrote:
> 
> Hello,
> has anyone encountered this problem with watertidy?
> ......... watertidy logfile ......
> 
>  *** Output H2o lines and  occupancy for nonbonded *** 301 250.710
> 
> 
> 
>   ** Average B values and bond length for H2Os
>   with 0 1 2 3 4 bonds to protein **
>  Number of bonds per H2O   0 Number of H2Os 301 Average B    27.321
> Average H bond     0.000
>  WATERTIDY:  Normal termination
>  Times: User:       1.8s System:    0.5s Elapsed:    0:01
> </pre>
> </html>
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> ERROR Can not find suitable unique chain name
> Try editting the file CCP4I_TOP/scripts/watertidy.script to add
> new chain names to the list called 'names'
> ***************************************************************************
> 
> 
> #CCP4I TERMINATION STATUS 0
> #CCP4I TERMINATION TIME 16 Feb 2001  10:32:59
> #CCP4I MESSAGE Task failed
> ----------------------------------------------------------------
> I have tried to add those id names but it did not help. I think
> the problem is somewhere else.
> 
>  Jan Dohnalek  (Mr.)
>  Institute of Macromolecular Chemistry
>  Heyrovskeho nam. 2, 162 06 Praha 6
>  Czech Republic (search in the middle of Europe)
>  Tel. : ++4202 20403205
>  Fax:  ++4202 35357981
>  E-mail: dohnalek@imc.cas.cz
> *******************************************************************


 I do something like this:

/y/ccp4/cadd/junk/distang xyzin $SCRATCH/prx377.brk <<eof
symm P21
RADI O 1.7 N 1.7 C 1.7 S 1.7 OW 1.7
dist vdw
FROM ATOM 1 to 15440
TO   ATOM 15441 to 20000
end
eof


#  Output file $CCP4_SCR/toxd_chnid.pdb will contain protein and
Sulphate
#  atoms followed by waters: Those close to protein will have been
renamed;
#  remainder will still have original name and chain ID.

2:
watertidy                          \
XYZIN $SCRATCH/prx377.brk \
XYZOUT $CCP4_SCR/prx377-wtidy1.pdb \
DISTOUT /y/ccp4/distang2-pol1.log \
<< END-watertidy
TITL Watertidy run on original pdb-file
SYMM P21
CHNID  A WATOUTID M RANGE 1 198
CHNID  B WATOUTID N RANGE 1 198
CHNID  C WATOUTID O RANGE 1 198
CHNID  D WATOUTID P RANGE 1 198
CHNID  E WATOUTID Q RANGE 1 198
CHNID  F WATOUTID R RANGE 1 198
CHNID  G WATOUTID S RANGE 1 198
CHNID  H WATOUTID T RANGE 1 198
CHNID  I WATOUTID U RANGE 1 198
CHNID  J WATOUTID V RANGE 1 198
WATID  W X Y Z
occw 0.01
SHELL 1
end
END-watertidy


-- 
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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
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