pdb file with duplicate atom names (Hydrogens)
I have taken over a high resolution set of protein data which has H atoms built in. For non-H atoms having 2 or three H atoms these H atoms each carry the same atom number in the pdb file. Phenix will not accept this format. Should I delete all H-atoms and reassign them in the next Phenix refinement run? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Hi Rex,
I have taken over a high resolution set of protein data which has H atoms built in. For non-H atoms having 2 or three H atoms these H atoms each carry the same atom number in the pdb file. Phenix will not accept this format. Should I delete all H-atoms and reassign them in the next Phenix refinement run?
if you got structure from somewhere (not Phenix) with H already present and Phenix does not recognize them, then it's best to remove H: phenix.reduce -trim model_with_H.pdb > model_no_H.pdb and then add them back phenix.ready_set model_no_H.pdb then use the new file with H from this point on. Note, you can do both steps using the GUI. Pavel
Hi Rex,
I have taken over a high resolution set of protein data which has H atoms built in. For non-H atoms having 2 or three H atoms these H atoms each carry the same atom number in the pdb file. Phenix will not accept this format. Should I delete all H-atoms and reassign them in the next Phenix refinement run?
if you got structure from somewhere (not Phenix) with H already present and Phenix does not recognize them, then it's best to remove H: phenix.reduce -trim model_with_H.pdb > model_no_H.pdb and then add them back phenix.ready_set model_no_H.pdb then use the new file with H added from this point on. Note, you can do both steps using the GUI. Pavel
participants (2)
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Pavel Afonine -
Rex Palmer