[phenixbb] Error in PDB Validation letter

Nigel W Moriarty NWMoriarty at lbl.gov
Sun May 2 11:50:08 PDT 2010


Raja

> 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...
>   
This is very interesting.  In my previous email, I had mixed up the 
codes AD, CD, GD, TD that the monomer library uses and the standard 
codes that PDB uses, DA, DC, ...  Ralf tells me that phenix.refine 
recognises these latter codes so there is something else up with the 
refinement.

You should follow Pavel's advice and check the .geo file.  It certainly 
seems like the refinement has not converged.

Nigel
> 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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>>
>>     
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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

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