Re: [ccp4bb]: refmac & idealize (u.k. : idealise)

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

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???? to the best of my knowledge this has always been an option?

  Go to GUI
Choose structure idealisation
Input pdb file - no mtz required
run for report and idealisation of geometry..


Here is the script the GUI generates..
refmac5 XYZIN /y/people/ccp4/projects/hpce/Marmod_MR_trial.pdb XYZOUT 
/y/people/ccp4/projects/hpce/Marmod_MR_trial_refmac1.pdb LIBOUT 
/y/people/ccp4/projects/hpce/Marmod_MR_trial.cif
make check NONE
make -
     hydrogen ALL -
     hout NO -
     peptide NO -
     cispeptide YES -
     ssbridge YES -
     chain NO -
     symmetry YES -
     sugar YES -
     connectivity NO -
     link NO
refi -
     type IDEA -
     resi MLKF -
     meth CGMAT -
     bref over
ncyc 5
bins 20
scal -
     type BULK -
     LSSC -
     ANISO -
     ncycles 10
weight -
     MATRIX 0.5
monitor MEDIUM -
     torsion 10.0 -
     distance 10.0 -
     angle 10.0 -
     plane 10.0 -
     chiral 10.0 -
     bfactor 10.0 -
     bsphere 10.0 -
     rbond 10.0 -
     ncsr 10.0
NOHARVEST
# External script file:
END


ernst@utbc08.cm.utexas.edu wrote:
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> 
> How does one get REFMAC or 5 to actually perform a geometry
> ONLY refinement.  neither will run without a valid hklin file.
> both insist on refining both xray and geom woth the
> refin ideal command.  If this never worked why has it been
> religiously perpetrated from the halcyon days of K&H?
> 
> woefully reminising on the kinder and simpler days of yesteryear-
> 
> Steve Ernst
> 
>