random seed to phenix.reflection_file_converter
Hi, Is there a way to provide a random seed to "phenix.reflection_file_converter" such that two runs will produce the same result (the same reflection set flagged as free)? What would be the syntax? For while I could only find for the context of refinement and simulated annealing ... Thanks, Jorge
Is there a way to provide a random seed to "phenix.reflection_file_converter" such that two runs will produce the same result (the same reflection set flagged as free)? What would be the syntax? For while I could only find for the context of refinement and simulated annealing ...
Sorry, the option is missing. However, you can easily patch the script to set the random seed. Please try this: cp $PHENIX/iotbx/iotbx/command_line/reflection_file_converter.py myrfc.py Edit myrfc.py and insert these lines between "import sys" and "def run():": from cctbx.array_family import flex import random flex.set_random_seed(0) random.seed(0) Then: phenix.python myrfc.py ... with the ... same arguments as before. Ralf
Hello I'm trying to minimize a (hypothetical) protein ligand complex where the ligand is very large. I can build a dictionary from the smiles description using elbow.builder (I love this capability!)). Can phenix perform minimization (or preferably simulated annealing) without real data? How? (This sort of thing could be done using xplor). (I have looked at the phenix documentation but didn't find the answer. I'm pretty sure the answer is in the documentation somewhere and I'm just not seeing it.) Thanks, Sue Dr. Sue A. Roberts Biochemistry & Biophysics University of Arizona 520 621 8171 [email protected]
Sue phenix.pdbtools --geometry-regularization does what you want. Nigel On 4/18/2008 1:42 PM, Sue Roberts wrote:
Hello
I'm trying to minimize a (hypothetical) protein ligand complex where the ligand is very large. I can build a dictionary from the smiles description using elbow.builder (I love this capability!)). Can phenix perform minimization (or preferably simulated annealing) without real data? How? (This sort of thing could be done using xplor). (I have looked at the phenix documentation but didn't find the answer. I'm pretty sure the answer is in the documentation somewhere and I'm just not seeing it.)
Thanks,
Sue
Dr. Sue A. Roberts Biochemistry & Biophysics University of Arizona 520 621 8171 [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Hi Sue, just to add to Nigel's reply... Yes, you can do geometry regularization using this command: phenix.pdbtools --geometry-regularization model.pdb There are two important parameters that define how far phenix.pdbtools will go with your model idealization: "max_iterations=500" and "macro_cycles=1" (500 and 1 are the default values). If you want to get an almost ideal model, then use something like this: "max_iterations=100" and "macro_cycles=1000". Cheers, Pavel. On 4/18/2008 1:42 PM, Sue Roberts wrote:
Hello
I'm trying to minimize a (hypothetical) protein ligand complex where the ligand is very large. I can build a dictionary from the smiles description using elbow.builder (I love this capability!)). Can phenix perform minimization (or preferably simulated annealing) without real data? How? (This sort of thing could be done using xplor). (I have looked at the phenix documentation but didn't find the answer. I'm pretty sure the answer is in the documentation somewhere and I'm just not seeing it.)
Thanks,
Sue
Dr. Sue A. Roberts Biochemistry & Biophysics University of Arizona 520 621 8171 [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (5)
-
iulekļ¼ interponta.com.br -
Nigel W. Moriarty -
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Sue Roberts