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
Raja _______________________________________________
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--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
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