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, [email protected] 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 [[email protected]] On Behalf Of Arnon Lavie
[[email protected]]
Sent: Friday, August 02, 2013 12:07 PM
To: [email protected]
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
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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: [email protected]<mailto:[email protected]>
http://www.uic.edu/labs/lavie/
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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: [email protected]
http://www.uic.edu/labs/lavie/
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