[phenixbb] Error in PDB Validation letter

[Raja Dey]

Dear Nigel,
                 Thanks for your reply. I understood the error with BML. I will try to fix that now. I am not clear what you suggested about the other error. Are you suggesting to change the nucleotides as follows:
DA to ADE
DC to CYT
and so on...

Actually I used 3 letter code for nucleotides in PHENIX refinement. Before submission to PDB I changed to DA, DC ....like this. Otherwise PDB deposition system can not recognize. Might be there is a way, so that I can avoid this hassle of changing this code for PDB deposition. Please tell me if I did anything wrong.
Thanks...

Raja 

----- Original Message -----
From: Nigel W Moriarty <NWMoriarty at lbl.gov>
Date: Sunday, May 2, 2010 9:43 am
Subject: Re: [phenixbb] Error in PDB Validation letter
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> 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 _______________________________________________
> >phenixbb mailing list
> >phenixbb at phenix-online.org
> >http://phenix-online.org/mailman/listinfo/phenixbb
> >
> >  
> 
> -- 
> 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
> 
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