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Re: [ccp4bb]: cannot calculate structure factors



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Dear Richard

I didn't see any other replies to your question. The warning you see
isn't from atomsf.lib but from the PDB reading library "rwbrook.f", and
the problem is most likely in your input PDB file - I suspect that the
atom name for "MG" is mis-aligned.

The atom name should be left justified in columns 13-16 of the PDB file,
since the contents of columns 13-14 are what the library uses for
comparision. Please check the format and let me know if this doesn't
solve the problem.

(Btw a description of the PDB format used by CCP4 can be found in the
CCP4 documentation, for example see
http://www.ccp4.ac.uk/dist/html/pdbformat.html#part1ato
for a description of the ATOM lines.)

Best wishes

Peter.

On Thu, 13 Feb 2003, Richard Baxter wrote:

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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Dear All,
> 
> I am tryaing to calculate structure factor amplitudes and phases for a
> model of the photosynthetic reaction center (B. viridis). This is a
> four-subunit polypeptide with many cofactors, and includes iron and
> magnesium ions.
> 
> SFALL fails with the following warning and error:
> 
> WARNING:  *UNKNOWN ATOMIC FORMFACTOR  MG  IN BCB   301*
> .....
> 
> The program run with command: sfall HKLOUT
> .....
> has failed with error message
>  SFALL:  No match for atom ID
> 
> It seems strange to me since the library
>   /opt/pkgs/ccp4-4.2.1/lib/data/atomsf.lib
> exists and is referenced by the program, and the log file shows no
> complaint for the iron atoms present in the haem cofactors that appear
> before the bacteriochlorophyll cofactors in my PDB file. Any advice is
> greatly appreciated,
> 
> regards,
> 
> Richard Baxter
> University of Chicago
> 
> 
> 

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