Re: [phenixbb] Error in PDB Validation letter

2 May 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 
Date: Sunday, May 2, 2010 9:43 am
Subject: Re: [phenixbb] Error in PDB Validation letter
To: PHENIX user mailing list 
...
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
[email protected]
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 : [email protected]
Fax   : 510-486-5909     Web   : CCI.LBL.gov
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________
phenixbb mailing list
[email protected]
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 : [email protected]
Fax   : 510-486-5909     Web   : CCI.LBL.gov