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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