difficulties with the refinement of a Cadmium containing pdb file
Hi all, I have some difficulties refining (what happens is an error status, i.e. no refinement taking place) of a coordinate file that contains Cadmium ions. The person here who has already refined a structure containing Cd ions using Phenix is not here at the moment (otherwise I would have asked him). In case you wonder: the CD is shifted 1 position to the left as is required for metal ions in a PDB. Phenix choked. So I ran ReadySet on the input pdb file and gave the output file to Phenix for the next attempt. Still failed, and the error message I get is: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 2 Please edit the PDB file to resolve the problem and/or supply a Cif file with matching restraints definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix_ready_set and phenix.elbow are available for creating restraints definitions (CIF files). Running phenix.elbow (phenix.elbow input_file.pdb --do-all) does not seem to do anything - no output file seems to be generated. Hence I am quite at loss here. Ready Set (from the gui) generated a file called name_of_the_coordinate_file.metal.edits , which is used by phenix for the next attempt but which does not seem to solve the problem. Thanks for any advice, Fred.
Hi Fred, Cd ions should create no problem for phenix.refine and you don't need to run any additional program... Make sure it is defined in your PDB file like this: HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN2+ ^^ Put the charge here Charge is optional, but note: phenix.refine does not infer the charge from the atom name. It has to appear in the PDB charge columns 79-80 as shown above. To make sure it is recognized correctly, look in phenix.refine log file - in the above example you would see something like this: Number of scattering types: 6 Type Number sf(0) Zn2+ 2 28.00 S 13 16.00 Na 2 11.00 O 240 8.00 N 113 7.00 C 442 6.00 sf(0) = scattering factor at diffraction angle 0. Pavel. On 4/7/11 5:53 AM, Vellieux Frederic wrote:
Hi all,
I have some difficulties refining (what happens is an error status, i.e. no refinement taking place) of a coordinate file that contains Cadmium ions. The person here who has already refined a structure containing Cd ions using Phenix is not here at the moment (otherwise I would have asked him). In case you wonder: the CD is shifted 1 position to the left as is required for metal ions in a PDB.
Phenix choked. So I ran ReadySet on the input pdb file and gave the output file to Phenix for the next attempt. Still failed, and the error message I get is:
Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 2 Please edit the PDB file to resolve the problem and/or supply a Cif file with matching restraints definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix_ready_set and phenix.elbow are available for creating restraints definitions (CIF files).
Running phenix.elbow (phenix.elbow input_file.pdb --do-all) does not seem to do anything - no output file seems to be generated. Hence I am quite at loss here. Ready Set (from the gui) generated a file called name_of_the_coordinate_file.metal.edits , which is used by phenix for the next attempt but which does not seem to solve the problem.
Thanks for any advice,
Fred. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Pavel, Indeed there was no charge on the Cd ions, and some of these Cd ions had improper annotations in columns 77-78. I must admit that I do not understand why these columns are used while the data (atom type) is provided before on the HETATM (or ATOM) record. Refining now (I hope). Fred. Pavel Afonine wrote:
Hi Fred,
Cd ions should create no problem for phenix.refine and you don't need to run any additional program... Make sure it is defined in your PDB file like this:
HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN2+
^^ Put the charge here
Charge is optional, but note: phenix.refine does not infer the charge from the atom name. It has to appear in the PDB charge columns 79-80 as shown above. To make sure it is recognized correctly, look in phenix.refine log file - in the above example you would see something like this:
Number of scattering types: 6 Type Number sf(0) Zn2+ 2 28.00 S 13 16.00 Na 2 11.00 O 240 8.00 N 113 7.00 C 442 6.00 sf(0) = scattering factor at diffraction angle 0.
Pavel.
Hi Fred, columns 77-78 define chemical element type. Atom label is not enough to unambiguously define it. For example, CA can be C-alpha or Calcium. Of course residue name can help further, but if you have a ligand then things get more complicated. Pavel. On 4/8/11 12:19 AM, Vellieux Frederic wrote:
Hi Pavel,
Indeed there was no charge on the Cd ions, and some of these Cd ions had improper annotations in columns 77-78. I must admit that I do not understand why these columns are used while the data (atom type) is provided before on the HETATM (or ATOM) record.
Refining now (I hope).
Fred.
Pavel Afonine wrote:
Hi Fred,
Cd ions should create no problem for phenix.refine and you don't need to run any additional program... Make sure it is defined in your PDB file like this:
HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN2+
^^ Put the charge here
Charge is optional, but note: phenix.refine does not infer the charge from the atom name. It has to appear in the PDB charge columns 79-80 as shown above. To make sure it is recognized correctly, look in phenix.refine log file - in the above example you would see something like this:
Number of scattering types: 6 Type Number sf(0) Zn2+ 2 28.00 S 13 16.00 Na 2 11.00 O 240 8.00 N 113 7.00 C 442 6.00 sf(0) = scattering factor at diffraction angle 0.
Pavel.
participants (2)
-
Pavel Afonine -
Vellieux Frederic