Dear Deniz,
In the past, I had similar problems caused by the fact that when the residue was “known” to ccp4, it would use the cif file from the ccp4 library instead of the cif I had created myself. You could check if this might be the case for you. You find the cif files under $CCP4/lib/data/monomers in the subdirectory with the first letter of the three-letter code of your ligand and check the CIF file with the same three-letter code as you are using.
However, it is possible that the ccp4 developers have resolved this issue by letting an externally provided cif file override the internal cif file.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von "Deniz Üresin"
Gesendet: Mittwoch, 3. April 2019 13:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] refmac5 problems with unnatural amino acid
Hello,
I'm trying to refine the structure of a protein mutant that has an unnatural amino acid in it. I created a restraint file for the AA and the mutation worked fine in COOT. But when I use refmac5 for refinement, it always changes the bond angle in the sidechain (an azide group, which should have a bond angle of 180°). I set the SD of the angle to 0 but that didn't help (the "refined" bond angle ends up somewhere between 120 and 150°).
Is there any other way to tell refmac5 to not alter that bond angle?
Thanks in advance,
Deniz Üresin
_________
Deniz Üresin
Institut für Biophysik
Johann Wolfgang Goethe-Universität Frankfurt am Main
http://www.biophys.uni-frankfurt.de/~bredenbeck/
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