Electrostatic potential map/Delphi/PDB2PQR
Dear All, I am facing a problem. I have a protein-RNA complex at 2A resolution I refined using TLS in Phenix. Now in the pdb file I have ANISOU line for every atom and probably many other errors. This is the reason I am not able to run Delphi or PDB2PQR to create potential electrostatic map. I removed already all water molecules and all heteratoms and ANISOU lines and RNA molecule. The program creating the phi file for the potentials does not work at all. Do you know any server which can correct any errors in the pdb file in order to run properly the program to create electrostatic map ?? Thanks a lot, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: [email protected] Url: http://www.embl.fr
Hello Ivan,
I am facing a problem. I have a protein-RNA complex at 2A resolution I refined using TLS in Phenix. Now in the pdb file I have ANISOU line for every atom
these ANISOU records are the result of TLS refinement and not an error. For example, see http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf from page 23, if you wish to learn about TLS.
and probably many other errors.
Specifically, what are these errors?
This is the reason I am not able to run Delphi or PDB2PQR to create potential electrostatic map. I removed already all water molecules and all heteratoms and ANISOU lines and RNA molecule. The program creating the phi file for the potentials does not work at all. Do you know any server which can correct any errors in the pdb file in order to run properly the program to create electrostatic map ??
I would talk to developers of respective programs. To me it sounds very odd that you need to do all these weird error-prone manipulations to your PDB file in order to run these programs. Pavel
Dear Ivan, as Pavel pointed out what appear to be errors to you are most likely bugs or short-comings in the downstream programs. PDB2PQR is not greatly sophisticated as it comes to PDB files (ANISOU records are for sure not errors). Did you try, though, the online-server or the standalone program? I have the impression that the server is more robust. Best, Tim On 10/21/2014 05:20 PM, Ivan IVANOV wrote:
Dear All, I am facing a problem. I have a protein-RNA complex at 2A resolution I refined using TLS in Phenix. Now in the pdb file I have ANISOU line for every atom and probably many other errors. This is the reason I am not able to run Delphi or PDB2PQR to create potential electrostatic map. I removed already all water molecules and all heteratoms and ANISOU lines and RNA molecule. The program creating the phi file for the potentials does not work at all. Do you know any server which can correct any errors in the pdb file in order to run properly the program to create electrostatic map ?? Thanks a lot, Ivan
-- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
participants (3)
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Ivan IVANOV -
Pavel Afonine -
Tim Gruene