Hi Nat, thanks for pointing it out. Actually, i'm preparing this for a small example script in order to include it in a practical seminar about the features and tools of the cctbx, so it is not that critical, but I would be glad to get some example code of how to use it properly, because my plans are to deepen into the use of these tools. Thanks again :) Claudia Millán ([email protected]) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain 2012/10/9 Nathaniel Echols

On Tue, Oct 9, 2012 at 1:08 AM, Claudia Millán Nebot wrote:

...

i'm trying to get an xray.structure object from a pdb file, as i'm interested on using both this and a Miller array coming from a reflection file to calculate correlation coefficients between Fobs and Fcalc.

I'm glad you were able to figure this out from the examples, but I have one caveat about your goal: if you're working with macromolecules, the Fcalc you get from an xray.structure object is going to be suboptimal because it won't contain any contribution from bulk solvent - only the point scatterers in the PDB file will be included. It may be necessary to use the (much messier) mmtbx.f_model API, which incorporates the bulk solvent (and also scales Fobs and Fcalc, although this isn't actually necessary for simple CCs). This isn't as well documented but I can give you some template code if you need it.

-Nat _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Claudia Millán ([email protected]) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain Hi again :) Thanks for the piece of code. I was looking at it rigth now and getting it to work, but i got this error: Traceback (most recent call last): File "simple_command_line_cc.py", line 47, in <module> run(sys.argv[1:]) File "simple_command_line_cc.py", line 31, in run prefer_anomalous=False) TypeError: __init__() got an unexpected keyword argument 'prefer_anomalous' I went to my cctbx_sources files, and look for the mmtbx/utils.py, and then realise that on there, the class cmdline_load_pdb_and_data, in is __init__, doesn't expect a prefer_anomalous keyword but a scattering_table one: def __init__ (self, args, master_phil, out=sys.stdout, process_pdb_file=True, create_fmodel=True, scattering_table="wk1995") Guess it maybe something related to the version of the cctbx i'm using? 2012/10/9 Nathaniel Echols

On Tue, Oct 9, 2012 at 5:35 AM, Claudia Millán Nebot wrote:

...

Hi Nat, thanks for pointing it out. Actually, i'm preparing this for a small example script in order to include it in a practical seminar about the features and tools of the cctbx, so it is not that critical, but I would be glad to get some example code of how to use it properly, because my plans are to deepen into the use of these tools.

I've attached a template which reads in the model and data, creates the fmodel object, and calculates CC(obs-calc). This is also in SVN now under mmtbx/examples/simple_command_line_cc.py, but I'll probably go back and modify it later to add more examples like calculating the model-map CC for an atom selection. There are of course other ways to write this, but it makes maximal use of Pavel's and my code for the really common, boring tasks like processing reflection files consistently, so it's a good place to start for writing programs with similar inputs.

-Nat

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Hi again :) Thanks for the piece of code. I was looking at it rigth now and getting it to work, but i got this error: Traceback (most recent call last): File "simple_command_line_cc.py", line 47, in <module> run(sys.argv[1:]) File "simple_command_line_cc.py", line 31, in run prefer_anomalous=False) TypeError: __init__() got an unexpected keyword argument 'prefer_anomalous' I went to my cctbx_sources files, and look for the mmtbx/utils.py, and then realise that on there, the class cmdline_load_pdb_and_data, in is __init__, doesn't expect a prefer_anomalous keyword but a scattering_table one: def __init__ (self, args, master_phil, out=sys.stdout, process_pdb_file=True, create_fmodel=True, scattering_table="wk1995") Guess it maybe something related to the version of the cctbx i'm using? Claudia Millán ([email protected]) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain 2012/10/9 Nathaniel Echols

On Tue, Oct 9, 2012 at 5:35 AM, Claudia Millán Nebot wrote:

...

Hi Nat, thanks for pointing it out. Actually, i'm preparing this for a small example script in order to include it in a practical seminar about the features and tools of the cctbx, so it is not that critical, but I would be glad to get some example code of how to use it properly, because my plans are to deepen into the use of these tools.

I've attached a template which reads in the model and data, creates the fmodel object, and calculates CC(obs-calc). This is also in SVN now under mmtbx/examples/simple_command_line_cc.py, but I'll probably go back and modify it later to add more examples like calculating the model-map CC for an atom selection. There are of course other ways to write this, but it makes maximal use of Pavel's and my code for the really common, boring tasks like processing reflection files consistently, so it's a good place to start for writing programs with similar inputs.

-Nat

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