Dear Gabriel (and the other members interested in how the issue was
solved; original post below):
You are this week's winner!! For getting the correct answer - it was
just a matter of editing the cif file and exchanging 'non-polymer' with
'peptide' - you get fame and glory on the CCP4 list, and the right to
play again.
Thanks a lot. Who said that there is nothing better than Google?
Arnon
On 8/2/13 12:01 PM, [log in to unmask] wrote:
> Arnon,
>
> This is most likely a problem in the CIF file. Did you define your modified residue as a 'non-polymer'?
> Take a look at how phospho-serine is defined and do something similar. We had similar issues and I think it was a trivial fix like this which worked.
>
> Good luck!
> Gabriel
>
>
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Arnon Lavie [[log in to unmask]]
> Sent: Friday, August 02, 2013 12:07 PM
> To: [log in to unmask]
> Subject: [ccp4bb] REFMAC5: linking a modified amino acid to adjacent residues
>
> Hi:
>
> Despite Google and several attempts, I am still having no success in getting Refmac5 to link a modified amino acid to its adjacent residues.
> Using sketcher, a cif file for the modified amino acid was generated.
> This cif file was used an input to Refmac5.
>
> The relevant part from the Refmac5 log file is shown below; note the "not be used" comment.
>
>
> INFO: link is found (not be used) dist= 0.776 ideal_dist= 1.332
>
> ch:BB res: 18 GLY at:C .->ch:Ba res: 19 THN at:N .
>
> INFO: link is found (not be used) dist= 1.686 ideal_dist= 1.240
>
> ch:BB res: 18 GLY at:O .->ch:Ba res: 19 THN at:N .
>
>
> I also added the link comment in the pdb file as shown below:
> LINK N THN B 19 C GLY B 18
> LINK C THN B 19 N LEU B 20
>
> Still, I fail to get a link between Gly18 to the modified residues THN19, and from it to the next residue Leu20.
>
> What trivial mistake am I making?
>
> Arnon
>
>
>
> --
> ***********************************************************
> Arnon Lavie, Professor
> Dept. of Biochemistry and Molecular Genetics
> University of Illinois at Chicago
> 900 S. Ashland Ave.
> Molecular Biology Research Building, Room 1108 (M/C 669)
> Chicago, IL 60607
> U.S.A.
> Tel: (312) 355-5029
> Fax: (312) 355-4535
> E-mail: [log in to unmask]<mailto:[log in to unmask]>
> http://www.uic.edu/labs/lavie/
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>
>
>
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--
***********************************************************
Arnon Lavie, Professor
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1108 (M/C 669)
Chicago, IL 60607
U.S.A.
Tel: (312) 355-5029
Fax: (312) 355-4535
E-mail: [log in to unmask]
http://www.uic.edu/labs/lavie/
***********************************************************
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