hi all I am trying to optimize the model, in which secondary structures are distorted and I did pdbtools , geometry regulatization , after optimization still the helices are distorted. Is it any tools in the phenix that could optimize the secondary structures alone in the pdb? Thanks ram
While I'm sure there's an easy work-around, I'm not coming up with it yet....obviously a problem in a ccp4-included library. Can I try linking to an older version somehow? Thanks, Christina christina@Fred:~/home$ phenix.pdbtools Traceback (most recent call last): File "/usr/local/bin/CCP4-6.1/ccp4-6.1.2/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/pdbtools.py", line 3, in ? from mmtbx import pdbtools File "/usr/local/bin/CCP4-6.1/ccp4-6.1.2/lib/cctbx/cctbx_sources/mmtbx/mmtbx/pdbtools.py", line 4, in ? from mmtbx import utils File "/usr/local/bin/CCP4-6.1/ccp4-6.1.2/lib/cctbx/cctbx_sources/mmtbx/mmtbx/utils.py", line 35, in ? from mmtbx.solvent import ordered_solvent File "/usr/local/bin/CCP4-6.1/ccp4-6.1.2/lib/cctbx/cctbx_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 13, in ? import mmtbx.f_model File "/usr/local/bin/CCP4-6.1/ccp4-6.1.2/lib/cctbx/cctbx_sources/mmtbx/mmtbx/f_model.py", line 4, in ? else: import phaser.phenix_adaptors.sad_target ImportError: No module named phenix_adaptors.sad_target
It is getting the "phenix.pdbtools" command from the CCP4 distribution which appears to have a non-compatible phaser version. I think the solution is very simple: source phenix_env (or phenix_env.sh) after the ccp4 setup so that you get phenix.pdbtools from our distribution. You can use which phenix.pdbtools to check where the command lives. Ralf
Works like a charm...thanks very much!
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From: Ralf W. Grosse-Kunstleve
Is it any tools in the phenix that could optimize the secondary structures alone in the pdb?
We don't have direct support for secondary structure restraints (although this came up quite often already). Using external tools you could prepare a file with "custom bond" restraints as described in the phenix.refine documentation. Note that the "slack" parameter is meant for hydrogen bond restraints, which I assume you want to use. Ralf
participants (3)
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Christina Bourne -
r n -
Ralf W. Grosse-Kunstleve