Raja Regarding the BML compound. This code is already taken for 4-BROMOPHENOL. You can look at it using phenix.reel --chemical-components=BML You can generate a new unused code thus elbow.get_new_ligand_code and one being with B thus elbow.get_new_ligand_code B Then the PDB with not compare you compound with the one currently known as BML. Regarding the deviations. The nucleotides denoted as DA, DC, DT, ... are not using the standard codes. This may mean that you generated new restraints that are not as accurate as the standard set in the restraints library. Either way, I suggest renaming the residues to the standard codes and re-refining. This will use the standard restraints and will likely approach the values mandated by the PDB. Nigel On 4/30/10 12:37 PM, Raja Dey wrote:
Hi, I am getting two errors in pdb validation report as follows: I think I need to use B-DNA constraint in the refinement. This is a 2.4 A data. How can I do that in PHENIX in cammand line promt.
Another thing is, I have a small molecule in the complex, which I called as BML. I think that's might be the problem. This is known as BML210. What I should call this compound? Should I also give a chain ID for this compound? See the errors given below.
*** Covalent Angle Values:
The overall RMS deviation for covalent angles relative to the standard dictionary is 1.4 degrees.
The following table contains a list of the covalent bond angles greater than 6 times standard deviation.
Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard Name ID Number Angle Value Deviation ------------------------------------------------------------------------------------------- -4.8 DA E 1 C1' - C2' - C3' 97.6 102.4 0.8 -5.8 DA E 2 C1' - C2' - C3' 96.6 102.4 0.8 3.3 DA E 2 N9 - C1' - O4' 111.6 108.3 0.3 -5.0 DC E 5 N1 - C1' - O4' 103.0 108.0 0.7 -5.1 DT E 6 C1' - C2' - C3' 97.3 102.4 0.8 -6.7 DT E 8 C1' - O4' - C4' 103.4 110.1 1.0 2.3 DT E 8 N1 - C1' - O4' 110.6 108.3 0.3 -4.5 DT E 11 N1 - C1' - O4' 103.5 108.0 0.7 -6.1 DA F 2 C1' - C2' - C3' 96.3 102.4 0.8 3.0 DA F 2 N9 - C1' - O4' 111.3 108.3 0.3 -5.3 DC F 5 N1 - C1' - O4' 102.7 108.0 0.7 -4.9 DT F 6 C1' - C2' - C3' 97.5 102.4 0.8 -4.5 DA F 10 N9 - C1' - O4' 103.5 108.0 0.7 -7.8 DA F 11 N9 - C1' - O4' 100.2 108.0 0.7
==> The following residues have extra atoms:
RES MOD#C SEQ ATOMS
BML( 100) N1 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 O2 N2 C20 N3 C7 C8 C9
ERROR: dissociated residue(s): BML 100
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