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
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
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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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