Hi, I'm using phenix for refinement and I keep getting an error. My DNA strand has a bromo-uridine in it and phenix.refine keeps crashing on this nucleotide. Here is the error: Number of atoms with unknown nonbonded energy type symbols: 40 "ATOM 2770 P BRU P 5 .*. P " "ATOM 2771 O1P BRU P 5 .*. O " "ATOM 2772 O2P BRU P 5 .*. O " "ATOM 2773 O5* BRU P 5 .*. O " "ATOM 2774 C5* BRU P 5 .*. C " "ATOM 2775 C4* BRU P 5 .*. C " "ATOM 2776 O4* BRU P 5 .*. O " "ATOM 2777 C1* BRU P 5 .*. C " "ATOM 2778 N1 BRU P 5 .*. N " "ATOM 2779 C6 BRU P 5 .*. C " ... (remaining 30 not shown) Here is what I have in my pdb: ATOM 2901 P BRU E 5 33.977 -16.324 24.303 1.00 27.21 P ATOM 2902 O1P BRU E 5 34.027 -15.724 22.919 1.00 28.22 O ATOM 2903 O2P BRU E 5 33.857 -15.340 25.393 1.00 25.06 O ATOM 2904 O5* BRU E 5 32.721 -17.236 24.418 1.00 28.02 O ATOM 2905 C5* BRU E 5 32.487 -18.228 23.495 1.00 28.50 C ATOM 2906 C4* BRU E 5 31.047 -18.347 23.082 1.00 32.59 C ATOM 2907 O4* BRU E 5 30.337 -18.858 24.152 1.00 28.61 O ATOM 2908 C1* BRU E 5 29.369 -17.891 24.535 1.00 29.63 C ATOM 2909 N1 BRU E 5 29.279 -17.855 25.962 1.00 29.72 N ATOM 2910 C6 BRU E 5 30.426 -17.755 26.799 1.00 30.57 C ATOM 2911 C5 BRU E 5 30.251 -17.738 28.232 1.00 30.89 C ATOM 2912 BR BRU E 5 31.869 -17.591 29.321 1.00 57.08 Br ATOM 2913 C4 BRU E 5 28.917 -17.845 28.826 1.00 30.70 C ATOM 2914 O4 BRU E 5 28.768 -17.825 30.033 1.00 29.36 O ATOM 2915 N3 BRU E 5 27.785 -17.945 27.981 1.00 29.36 N ATOM 2916 C2 BRU E 5 27.961 -17.966 26.552 1.00 29.05 C ATOM 2917 O2 BRU E 5 26.994 -18.064 25.848 1.00 35.29 O ATOM 2918 C3* BRU E 5 30.464 -17.006 22.751 1.00 34.58 C ATOM 2919 C2* BRU E 5 29.845 -16.605 23.968 1.00 33.10 C ATOM 2920 O3* BRU E 5 29.526 -17.213 21.768 1.00 37.93 O I have already run a BRU molecule through ReadySet and when I use the cif file generated from this phenix.refine will run through but when the Bromine atom is in the structure has a large negative density peak in the Fo-Fc map. I think it may just be a naming thing. BRU is already in the monomer library so I don't understand why I get an error at first also without the readyset cif file. Any suggestions? Thanks, Krystle
On Fri, May 20, 2011 at 2:42 PM, Krystle Williams McLaughlin < [email protected]> wrote:
I have already run a BRU molecule through ReadySet and when I use the cif file generated from this phenix.refine will run through but when the Bromine atom is in the structure has a large negative density peak in the Fo-Fc map.
This could just be radiation damage - assuming the Br is in the correct position as judged by the 2Fo-Fc map, it doesn't have anything to do with the restraints used. I don't know if there's a reference for this, but I was told that brominated nucleotides are extremely sensitive to radiation damage, much worse than SeMet. Did you use this for phasing? I think it may just be a naming thing. BRU is already in the monomer
library so I don't understand why I get an error at first also without the readyset cif file.
It isn't in the version of the monomer library we distribute - many of the files in the full version are incomplete, and we don't include those. ReadySet does have access to the Chemical Components Database definition of BRU, however, which it probably used to make the restraints. -Nat
participants (2)
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Krystle Williams McLaughlin -
Nathaniel Echols