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

[Garib N Murshudov <garib@ysbl.york.ac.uk>]

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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:
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> ***          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