Hi Pavel,
I enclosed the line below:
ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Z
I also tried with
ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Zn
None worked.
Raja
----- Original Message -----
From: Pavel Afonine
Hi Raja,
normally phenix.refine should recognize Zn atoms without any problems and you don't need run elbow for this. If it doesn't, that most likely means your PDB file is ill-formatted (for example, no element type defined in 77(?) column). Could you please send me copy of the ATOM line from your PDB file containing Zn so I can tell what is wrong?
Pavel.
On 5/26/09 12:31 PM, Raja Dey wrote:
Dear Friends, I have Zn atoms in my pdb file. So, I think I need to run elbow to create the cif otherwise refinement stops. I did the following and got the error as follows:
phenix.elbow generate_easy_r4.pdb --do-all
-----------------------------------------------------------------
electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3 - Nigel W. Moriarty ([email protected]) -----------------------------------------------------------------
Random number seed: 664322001 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing
Parsing Parsing P
No molecule read
Use --all-residues to view residues if this is a PDB file
Can anyone suggests at this point, what I should do? Thanking you in advance...
Raja
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