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CCP4BB  March 2009

CCP4BB March 2009

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Subject:

Re: Error message while refining protein-DNA complex structure in Refmac5

From:

E rajakumar <[log in to unmask]>

Reply-To:

E rajakumar <[log in to unmask]>

Date:

Tue, 17 Mar 2009 14:04:52 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (101 lines)

Dear Garib
Thank you very much as you suggested, I removed SCALE
card in the pdb file, then it is running smothly.

Rajakumara


--- Garib Murshudov <[log in to unmask]> wrote:

> It seems that something may be wrong with your input
> file.
> Specifically with the SCALE card in the pdb file.
> Could you please
> remove SCALE lines from the pdb and try again. If it
> does not help
> then could you please send me your pdb file and I
> will try to sort out.
>
> Garib
>
> On 16 Mar 2009, at 22:43, E rajakumar wrote:
>
> > Dear All
> > I am refining proitein-DNA complex structure in
> > Refamac5. When I used coordinate file containing 2
> > bases less, then the refinement is running smoth
> and
> > perfect. But when I built 2 exta bases to the
> existing
> > DNA in the coot then refinement is failed with the
> > following error message.
> >
> > /usr/local/ccp4-6.1.0/bin/refmac5
> >
>
XYZIN"/usr6/rajkumar/APS/hem/mar9/H11112/molrep/BCDNA-built2-NCS-
>
> > refm2.pdb"
> > XYZOUT "/tmp/rajkumar/hemCG_19_2_pdb_1.tmp" HKLIN
> >
>
"/usr6/rajkumar/APS/hem/mar9/H11112/molrep/P6122.mtz"
> > HKLOUT "/tmp/rajkumar/hemCG_19_3_mtz_1.tmp" LIBOUT
> >
>
"/usr6/rajkumar/APS/hem/mar9/H11112/molrep/hemCG_19_lib.cif"
> >
> > has failed with error message
> > At line 2486 of file
> > /usr/local/xtal/ccp4-6.1.0/src/refmac5_/make_PDB.f
> > Fortran runtime error: Bad value during floating
> point
> > read
> >
> > It seems there is error in LIB file generation.
> > Coordinate format and atom labelling is accoring
> to
> > refmac convention.
> >
> > Please can anybody suggest me how do I
> trooubleshoot.
> >
> > Thanking you
> > Rajakumara
> >
> >
> >
> >
> > E. Rajakumara
> > Postdoctoral Fellow
> >  Strcutural Biology Program
> >  Memorial Sloan-Kettering Cancer Center
> >  New York-10021
> >  NY
> >  001 212 639 7986 (Lab)
> >  001 917 674 6266 (Mobile)
> >
> >
> >
> >      Get your preferred Email name!
> > Now you can @[log in to unmask] and @[log in to unmask]
> > http://mail.promotions.yahoo.com/newdomains/aa/
> >
>
>


E. Rajakumara
Postdoctoral Fellow
  Strcutural Biology Program
  Memorial Sloan-Kettering Cancer Center
  New York-10021
  NY
  001 212 639 7986 (Lab)
  001 917 674 6266 (Mobile)



      Get your new Email address!
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