[phenixbb] Error in PDB Validation letter

[Nigel W Moriarty]

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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909     Web   : CCI.LBL.gov