Hi, Is there a convenient tool to obtain ADP for each chain or ligand or a selective group? phenix.model_vs_data only gives an averaged ADP for everything and it takes really long. Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================
Hi Jason,
Is there a convenient tool to obtain ADP for each chain or ligand or a selective group? phenix.model_vs_data only gives an averaged ADP for everything and it takes really long. Thanks.
phenix.pdbtools model.pdb --show-adp-statistics will show you more detailed (in some sense) ADP statistics. However, it will not distinguish chains, etc. If you want this statistics available per selected atoms (like chains), then it will take two steps: 1) Make a PDB file with atoms in question: phenix.pdbtools model.pdb keep="chain A and resseq 1:100" 2) Compute B-factor statistics for the new file obtained at step "1": phenix.pdbtools model_new.pdb --show-adp-statistics I will add more functionality to phenix.pdbtools so in future it will do it all in one go. Pavel.
Hi Pavel,
It sounds doable. One minor point is that for ligand, phenix.pdbtools needs
restrain file. For ADP statistics, it seems asking a bit too much.
On Wed, Apr 6, 2011 at 2:15 PM, Pavel Afonine
Hi Jason,
Is there a convenient tool to obtain ADP for each chain or ligand or a
selective group? phenix.model_vs_data only gives an averaged ADP for everything and it takes really long. Thanks.
phenix.pdbtools model.pdb --show-adp-statistics
will show you more detailed (in some sense) ADP statistics. However, it will not distinguish chains, etc.
If you want this statistics available per selected atoms (like chains), then it will take two steps:
1) Make a PDB file with atoms in question:
phenix.pdbtools model.pdb keep="chain A and resseq 1:100"
2) Compute B-factor statistics for the new file obtained at step "1":
phenix.pdbtools model_new.pdb --show-adp-statistics
I will add more functionality to phenix.pdbtools so in future it will do it all in one go.
Pavel.
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-- ====================== Jason Structural Biology Department University of Pittsburgh ======================
Hi Jason,
It sounds doable. One minor point is that for ligand, phenix.pdbtools needs restrain file. For ADP statistics, it seems asking a bit too much.
naively it may seem too much. But when you do selection on your model: for example, select certain protein atoms, water, ions, ligands, etc.. the selection machinery needs to know what is what (at the very deep basic level), and obviously the PDB file alone is not enough of source of such information, therefore the library is needed. So if your PDB file contains a ligand that PHENIX "doesn't know", then you need to define it first before requesting any manipulation on it. Your are right, you don't need it for ADP statistics, but in my example I was doing selection on a PDB file, so if you want to repeat anything similar your need a CIF file for your ligand that is strange to PHENIX. Good luck, Pavel.
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Pavel Afonine