Re: [ccp4bb]: Refmac_5.1.24 for Linux screws up histidine conformation ??

[Martin Moche <martin@alfa.mbb.ki.se>]

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Yes, the hydrogens was causing the trouble !

So either remove them all, or put their occupancy to 1, as suggested by Roger
Dodd works.

Thanks a lot !

Martin

Garib N Murshudov wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Hi
>
> Are you using hydrogens. Add all hydrogens. If yes that may be reason. Remove
> hydrogens and see what happens
>
> Garib
>
> On Friday 01 November 2002 14:28, Martin Moche wrote:
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> > Dear CCP4 Users,
> >
> > I'm using Refmac5 version 5.1.24 under Linux to refine a structure with
> > six chains in the asymmetric unit using strong NCS restraints. After the
> > refmac5 run none of the nine imidazole rings of my histidine residues
> > fulfill the strong NCS but instead they are all rotated around the CB-CG
> > bond having completely different conformations ?
> >
> > I have previously used refmac5 to refine the very same pdb-file without
> > problems using the 5.0.32 version under Unix ???
> >
> > Has someone encountered the same problem as me and what can I do about
> > it ?
> > I give my input file in case there is something obvious
> >
> > Best Regards
> >
> > Martin Moche
> > Karolinska Institutet
> > Stockholm
> > Sweden
> >
> > **************************************************************************'
> >
> > #!/bin/csh -f
> > start:
> > set name = johan_
> > set last = 0
> > set cycles = 1
> > set count = 0
> > set title  = ' Testing Refmac_5.1.24 '
> > set resol  = '25 2.4'
> > set cell   = '81.774  145.21  192.88   90.000   90.000   90.000'
> > set symm   = 'P212121'
> > set data = '/nfs/disk2/martin/desa/data/data_scalepack.mtz'
> > while ($count != $cycles)
> > echo
> > '*******************************************************************'
> > echo  $count
> > echo
> > '*******************************************************************'
> > @ curr = $last + 1
> >
> > refmac5 \
> > HKLIN  $data \
> > HKLOUT   ${name}${curr}.mtz \
> > XYZIN    ${name}${last}.pdb \
> > XYZOUT   ${name}${curr}.pdb \
> > TLSIN tls.in \
> > << eor
> > NONX NCHAIns 6 CHNID A B C D E F NSPANS 1 18 366 1
> > LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag
> > LABO FC=FC PHIC=PHIC  FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT
> > SOLVENT VDWP 1.4 IONP 0.80 RSHR 0.8
> > WEIG MATR 0.03
> > REFI TLSC 20
> > BFACtor SET_to 40
> > REFInement TYPE RESTrained RESOLUTION  25.0 2.4
> > REFInement RESIdual MLKF
> > REFInement BREFinement ISOTropic
> > MONI MEDI
> > SCALE LSSCale FIXBulk  BBULk 200
> > SCAL LSSC ANISOT
> > SCAL TYPE BULK
> > NCYC 20
> > eor
> > #
> > if ($status) exit
> > @ last++
> > @ count++
> > end
> >
> > ***************************************************************************
> >********
>
> --
> Dr. Garib N Murshudov, YSBL, Chemistry Dp, Univerisyt of York
> Tel: (01904) 328252