[phenixbb] Estimation of ligand binding affinity by occupancy refinement

Terwilliger, Thomas C terwilliger at lanl.gov
Tue May 1 07:08:13 PDT 2012


Hi Nora,

I'm sorry for the trouble!  I tried your fixed ensemble command out with the current phenix and it ran fine for me.  Could you possibly try downloading a very recent nightly build and see if that fixes the problem?  If not, please let me know and we'll fix it.

All the best,
Tom T

parameter file:
...
  fixed_ensembles {
    fixed_ensembleID_list = ensemble_1
    fixed_euler_list = 87.09 64.28 257.24
    fixed_frac_list = 0.54 0.079 0.069
    fixed_frac_list_is_fractional = True
  }


output:
...
Adding Ensemble  ensemble_1  as fixed solution with:
 Euler angles:  [87.09, 64.28, 257.24]
 Coords (orthogonal A):  [0.54, 0.079, 0.069]
Keeping all solutions within 75.00 percent of the best solution
Only searching in Space Group given in MTZ file plus opposite hand if enantiomorphic)
Trying only input search order
Disabling consistency check for all ensembles
Starting PHASER ...

Note: the "orthogonal A" is a typo I just noticed and I have now fixed that to say "fractional" in this case...

________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Nora Cronin [Nora.Cronin at icr.ac.uk]
Sent: Tuesday, May 01, 2012 7:32 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Estimation of ligand binding affinity by occupancy refinement

I'm having a small problem with format - entering fixed_ensembles in automr:

my input:

  fixed_ensembles {
    fixed_ensembleID_list = "ensemble_1"
    fixed_euler_list = 87.09  64.28 257.24
    fixed_frac_list = 0.540  0.079  0.069
    fixed_frac_list_is_fractional = True
  }

Phenix output:

Adding Ensemble  ensemble_1  as fixed solution with:
 Euler angles:  [87.09, 64.28, 257.24]
 Coords (orthogonal A):  [0.54, 0.079, 0.069]
*************ERROR ENDING *******************

****************************************
AutoMR Input failed
Python argument types in
    SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool)
did not match C++ signature:
    addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double)
****************************************
*************ERROR ENDING *******************
[1


In addition to fixed two solutions is it necessary to repeat the key phrases or can one add to "fixed_euler_list" in groups of three (do they need to be comma delimited?


Nora



Dr N B Cronin
X-Ray Laboratory Manager               Tel. (+44) 020 7153 5445
Section of Structural Biology             Fax. (+44) 020 7153 5456
Chester Beatty Laboratories             mobile: (+44) 07787554059
The Institute of Cancer Research
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