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Re: [ccp4bb]: Disulfides between NCS related molecules



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Hi Felix,

Problem seems to be with format (It is pdb requirement). See below for format 
of SSBOND. SYMM1 and SYMM2 are left justified. In your case SYMM1 starts at 
position 61 and it should start at 60. Here is corrected vesion which should 
work.
SSBOND   3 CYS A  427    CYS B  427                         1555   3646

Regards
Garib

c 1 -  6       Record name     "SSBOND"
c
c 8 - 10       Integer         serNum         Serial number.
c
c12 - 14       LString(3)      "CYS"          Residue name.
c
c16            Character       chainID1       Chain identifier.
c
c18 - 21       Integer         seqNum1        Residue sequence number.
c
c22            AChar           icode1         Insertion code.
c
c26 - 28       LString(3)      "CYS"          Residue name.
c
c30            Character       chainID2       Chain identifier.
c
c32 - 35       Integer         seqNum2        Residue sequence number.
c
c36            AChar           icode2         Insertion code.
c
c60 - 65       SymOP           sym1           Symmetry operator for 1st 
residue.
c
c67 - 72       SymOP           sym2           Symmetry operator for 2nd 
residue.


On Wednesday 29 May 2002 4:27 pm, Vajdos, Felix wrote:
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Can someone explain to me how to establish a disulfide link for refmac5
> between two NCS related monomers?  The problem is that the disulfide occurs
> between molecule A and a molecule B in a different asymmetric unit.  I
> thought I understood how to do this from Eleanor's response to a similar
> question last year regarding links, but I cannot seem to make it work.
>
> I have tried inserting the following SSBOND statement in my pdb file:
>
> SSBOND   3 CYS A  427    CYS B  427                          1555   3646
>
> The symmetry and origin shift I got from the output of act, (symmop 3,
> origin shift of 1,-1,1).
>
> I have also tried including in my input script:
> MAKE SS Y
> MAKE SYMM Y
>
> Neither of these seems to work.  Refmac picks up two intramolecular
> disulfides fine, but seems to ignore this intermolecular disulfide.
>
>
> Thanks in advance!
>
>
> Felix F. Vajdos
> Pfizer Inc
> Eastern Point Road
> MS 4039
> Groton, CT  06340
>
> 860-715-6504
>
> The full input script is as follows:
>
> refmac5 \
> HKLIN   $inmtz \
> HKLOUT   $REFMAC_SCR/${name}${curr}.mtz \
> XYZIN   ./${name}${last}.pdb \
> XYZOUT  ./${name}${curr}.pdb \
> LIBIN   ${cplib} \
> << eor
> LABIN FP=F SIGFP=SIGF  FREE=FreeR_flag
> LABO FC=FC PHIC=PHIC    FWT=2FOFCWT PHWT=PH2FOFCWT -
>                      DELFWT=FOFCWT  PHDELWT=PHFOFCWT
> ! We don't want any harvesting for cif files !
> NOHARVEST
> MAKE CHECK NONE
> MAKE HYDR All
> MAKE SS Y
> MAKE SYMM Y
> !
> REFI TYPE RESTrained RESOLUTION  ${reslim}
> REFI RESI MLKF
> REFI BREF ISOTropic
> !
> !
> WEIGHT MATRIX ${matwt}
> DAMP 0.5 0.5
> !Scaling parameters:, use BAbinet's bulk solvent type scaling
> SCAL TYPE BULK
> ! and do anisotropic scaling
> SCALE LSSC ANIS
> ! estimate sigmaAs
> SCALE MLSC
> NCYC 20
> MONI MEDI
> BINS 20
> end
> eor
>
>
>
>
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-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 432565